Question: 8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
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gravatar for Sarah JugurnauthLittle
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Sarah JugurnauthLittle20 wrote:
Dear Bernard, regarding the last part of your question, it might help you to know about packages CGHtest (http://www.few.vu.nl/~mavdwiel/CGHtest.html) or CNVtools (http://www.bioconductor.org/packages/release/bioc/html/CNVtools.html) that can both be used for looking at genetic association of calls. Date: Tue, 6 Aug 2013 09:12:05 -0700 (PDT) From: "Bernard North [guest]" <guest@bioconductor.org> To: bioconductor at r-project.org, b.v.north at qmul.ac.uk Cc: CGHcall Maintainer <mark.vdwiel at="" vumc.nl=""> Subject: [BioC] CGHCall problems Message-ID: <20130806161205.C269B143590 at mamba.fhcrc.org> Dear All, I am using CGHcall to segment and call aCGH copy number data. My understanding is that the segmentation step of CGHcall is the same CBS method used in DNAcopy. CGHcall has a function called "calls" which has segments as rows (defined as start probe to end probe) and columns for each sample with the elements being calls. Given that DNAcopy has a different segmentation for each sample how is the segmentation in allcalls decided upon ? Calls is run as allcalls<-data.frame(calls(result)) where result is the final CGHCall object as per the vignette Also does CGHcall provide pvalues or qvalues to test if any regions are recurrently amplified or deleted over samples ? -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of bioconductor-request@r-project.org Sent: 07 August 2013 11:00 To: bioconductor at r-project.org Subject: Bioconductor Digest, Vol 126, Issue 7 Send Bioconductor mailing list submissions to bioconductor at r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/bioconductor or, via email, send a message with subject or body 'help' to bioconductor-request at r-project.org You can reach the person managing the list at bioconductor-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioconductor digest..." Today's Topics: 1. Limma\'s roast() does not accept weigths in combination with block (Gordon K Smyth) 2. Re: XCMS query regarding mzXML (Reema Singh) 3. HTqPCR problem with ttestCtData function (Ruben Dries) 4. Re: XCMS query regarding mzXML (Laurent Gatto) 5. Re: request (Wolfgang Huber) 6. Re: RNASeq:- getting Zero Count (Valerie Obenchain) 7. Extracting overlapping gene names from a list of peaks (Patrick Schorderet) 8. CGHCall problems (Bernard North [guest]) 9. Re: Extracting overlapping gene names from a list of peaks (James W. MacDonald) 10. Re: request (Alexey Moskalev) 11. Re: DNAStringSetList can't coerce a list? (Taylor, Sean D) 12. fRMA package (Li Liu) 13. Re: ggbio: Data stored twice in 'GGbio' object (Michael Lawrence) 14. Re: fRMA package (Dan Tenenbaum) 15. Re: request (Laurent Gatto) 16. Re: request (Alexey Moskalev) 17. Re: request (Wolfgang Huber) 18. Re: request (Steve Lianoglou) 19. Re: ggbio facet_gr example sought (Michael Lawrence) 20. Re: ggbio: Data stored twice in 'GGbio' object (Julian Gehring) 21. Re: fRMA package (Li Liu) 22. Re: fRMA package (Dan Tenenbaum) 23. Re: Extracting overlapping gene names from a list of peaks (Michael Lawrence) 24. Re: fRMA package (Li Liu) 25. Re: fRMA package (Dan Tenenbaum) 26. Re: ggbio facet_gr example sought (Tengfei Yin) 27. ??: an error in AnnotationForge (joseph) 28. beadarray library: perBeadFile (Nogales Vilardell) 29. ??: an error in AnnotationForge (joseph) 30. topGO question (Datong Wang) 31. Re: ggbio facet_gr example sought (Cook, Malcolm) 32. basic query to make groups .. (ALok) ---------------------------------------------------------------------- Message: 1 Date: Tue, 6 Aug 2013 21:17:28 +1000 (AUS Eastern Standard Time) From: Gordon K Smyth <smyth@wehi.edu.au> To: ssehztirom at gmail.com Cc: Bioconductor mailing list <bioconductor at="" r-project.org=""> Subject: [BioC] Limma\'s roast() does not accept weigths in combination with block Message-ID: <pine.wnt.4.64.1308062109130.7100 at="" pc975.wehi.edu.au=""> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > Date: Mon, 5 Aug 2013 03:36:49 -0700 (PDT) > From: "Moritz Hess [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, ssehztirom at gmail.com > Subject: [BioC] Limma\'s roast() does not accept weigths in > combination with block > > Dear All, > > I am conducting enrichment tests using Limma's roast() function. As I > am investigating RNA-Seq data, I have to introduce the weights > calculated by voom(). Without a blocking variable, roast() runs without > an itch but when I introduce a blocking variable (with or without > correlation within blocks), roast() halts and returns "Can't use block > with weights". Is the combination of weights and blocking variables in > roast() generally impossible Not impossible, but requires some careful special case programming. > and if not, will it be possible in upcomming releases of limma? Yes, but not in the next few weeks. Gordon > Thank you very much in advance, > > Moritz > > -- output of sessionInfo(): > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel splines stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0 > [5] BiocGenerics_0.6.0 statmod_1.4.17 edgeR_3.2.3 limma_3.16.5 > > loaded via a namespace (and not attached): > [1] annotate_1.38.0 AnnotationDbi_1.22.6 compiler_3.0.1 > [4] DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 > [7] grid_3.0.1 IRanges_1.18.1 RColorBrewer_1.0-5 > [10] RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 > [13] tools_3.0.1 XML_3.98-1.1 xtable_1.7-1 > > > -- ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}} ------------------------------ Message: 2 Date: Tue, 6 Aug 2013 18:42:26 +0530 From: Reema Singh <reema28sep@gmail.com> To: Laurent Gatto <lg390 at="" cam.ac.uk=""> Cc: bioconductor <bioconductor at="" r-project.org=""> Subject: Re: [BioC] XCMS query regarding mzXML Message-ID: <caehmz4tq0sxrhud-dw6ngmy-lozasf0c491u_omqcm1z2aqo4g at="" mail.gmail.com=""> Content-Type: text/plain Dear Laurent, Thank you for your reply. It' sworking fine with "PAe000002_mzXML_201106211454.tar.gz" this dataset on my machine. But when I have used "PAe000030_mzXML_201104131929.tar.gz", I got error. Here's the complete command and sessioninfo. library(xcms) files <- list.files("PAe000030",recursive=TRUE,full.names=TRUE) files [1] "PAe000030/hui_serum10_full.mzXML" [2] "PAe000030/hui_serum16_full.mzXML" [3] "PAe000030/hui_serum17_full.mzXML" [4] "PAe000030/hui_serum18_full.mzXML" . > xr<-xcmsRaw(files[1]) Warning message: In `profStep<-`(`*tmp*`, value = 1) : MS1 scans empty. Skipping profile matrix calculation. > xr<-xcmsRaw(files) Error in file(con, "rb") : invalid 'description' argument In addition: Warning message: In if (!file.exists(filename)) return(FALSE) : the condition has length > 1 and only the first element will be used > xr <- xcmsSet(files) Error in x[1]:x[2] : NA/NaN argument > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] xcms_1.36.0 Biobase_2.20.1 BiocGenerics_0.6.0 mzR_1.6.2 [5] Rcpp_0.10.4 loaded via a namespace (and not attached): [1] codetools_0.2-8 Kind Regards On Tue, Aug 6, 2013 at 3:23 PM, Laurent Gatto <lg390 at="" cam.ac.uk=""> wrote: > Dear Reema, > > On 6 August 2013 10:22, Reema Singh <reema28sep at="" gmail.com=""> wrote: > > Dear All, > > > > I am trying to import .mzXML files using XCMS package. I have tried it > with > > two different data set ( > > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030 ) and > > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe0000< > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030>02). > > After extracting .mzXML files, when i tried to import them using XCMS, I > > got this output. > > *PAe000002* > > files <- list.files("TEST", recursive=TRUE,full.names=TRUE) > >> xr<-xcmsRaw(files[1]) > >> xr > > An "xcmsRaw" object with 2070 mass spectra > > > > Time range: 120-5879.1 seconds (2-98 minutes) > > Mass range: 400.0667-1399.9995 m/z > > Intensity range: 1-465033000 > > > > MSn data on 0 mass(es) > > with 0 MSn spectra > > Profile method: bin > > Profile step: 1 m/z (1001 grid points from 400 to 1400 m/z) > > > > Memory usage: 34.4 MB > > > > *PAe000030* > > > >> files1 <- list.files("TEST1", recursive=TRUE,full.names=TRUE) > >> xr1<-xcmsRaw(files1[1]) > > Warning message: > > In `profStep<-`(`*tmp*`, value = 1) : > > MS1 scans empty. Skipping profile matrix calculation. > >> xr1 > > An "xcmsRaw" object with 0 mass spectra > > > > MSn data on 0 mass(es) > > with 0 MSn spectra > > Profile method: bin > > Profile step: no profile data > > > > Memory usage: 0.00481 MB > >> > > > > Now My question is Why One dataset is successfulyy imported, whereas in > the > > same dataset got some warnings and datset with zero masses?. > > > > I would appreciate any help. > > First, we do not know exactly what files you are using for your test. > Reading all of the PAe000030 mzXML files works well on my computer, > indicating that it is likely not a mzXML issue as such. > > As the warning message suggests, the MS1 scans of that particular > mzXML file are empty, which terminates the processing. Have you had > more luck with another file from that experiment? You might want to > check the offending mzXML file - it might indeed be valid yet 'empty'. > > Hope this helps, > > Laurent > > > Kind Regards > > > > > > -- > > Reema Singh > > PhD Scholar > > Computational Biology and Bioinformatics > > School of Computational and Integrative Sciences > > Jawaharlal Nehru University > > New Delhi-110067 > > INDIA > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Laurent Gatto > - http://proteome.sysbiol.cam.ac.uk/lgatto/ > Cambridge Centre for Proteomics > - http://www.bio.cam.ac.uk/proteomics > Using R/Bioconductor for proteomics data analysis > - http://lgatto.github.io/RforProteomics/ > -- Reema Singh PhD Scholar Computational Biology and Bioinformatics School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi-110067 INDIA [[alternative HTML version deleted]] ------------------------------ Message: 3 Date: Tue, 6 Aug 2013 15:49:22 +0200 From: Ruben Dries <rubendries@gmail.com> To: bioconductor at r-project.org Subject: [BioC] HTqPCR problem with ttestCtData function Message-ID: <478085E4-536C-411A-A114-F55FA895A72E at gmail.com> Content-Type: text/plain Dear, I'm having a problem with the ttestCtData function from the HTqPCR package, which I use to analyze my BioMark Fluidigm data. In most cases there is no problem: > qDE.ttest.Nanog <- ttestCtData(q.norm[,c(1:9)], groups = conditions[c(1:9)], calibrator = "R-L_KD", stringent = FALSE) > head(qDE.ttest.Nanog, n=2) genes feature.pos t.test p.value adj.p.value ddCt FC meanCalibrator meanTarget categoryCalibrator categoryTarget 40 Nanog feature30 -16.290155 2.477252e-05 0.002204754 1.2277206 0.4269915 15.50882 16.73654 OK OK 84 Zcchc12 feature71 6.271628 4.370851e-04 0.019450286 -0.5513761 1.4654829 16.03707 15.48569 OK OK However sometimes I get this error > write.table(qDE.ttest.Nanog, file = "/Users/ruben/Dropbox/Data/qPCR/ results/BioMark/Fluidigm4/ND2_fluid4/Ttest/ND2_ttest_Nanog.txt") > qDE.ttest.Rest <- ttestCtData(q.norm[,c(1:5,10:13)], groups = conditions[c(1:5,10:13)], calibrator = "R-L_KD", stringent = FALSE) Error in t.test.default(x[, g1], x[, g2], alternative = alternative, paired = paired, : data are essentially constant However when I change the normalization from quantile normalization (q.norm) to for example norm.rankinvariant (nr.norm) this error doesn't occur anymore. All of the samples are different, I compare 4 biological target replicates to 4 from the control. Could it be due to the quantile normalization? And would it be ok if I used the norm.rankinvariant normalization if I encounter this error? Best regards, Ruben [[alternative HTML version deleted]] ------------------------------ Message: 4 Date: Tue, 6 Aug 2013 15:28:17 +0100 From: Laurent Gatto <lg390@cam.ac.uk> To: Reema Singh <reema28sep at="" gmail.com=""> Cc: bioconductor <bioconductor at="" r-project.org=""> Subject: Re: [BioC] XCMS query regarding mzXML Message-ID: <ca+unozhpp0347vki1u+0ymzbunstknyt=nyrqkfm+7-6tddg3w at="" mail.gmail.com=""> Content-Type: text/plain; charset=ISO-8859-1 On 6 August 2013 14:12, Reema Singh <reema28sep at="" gmail.com=""> wrote: > Dear Laurent, > > Thank you for your reply. > > It' sworking fine with "PAe000002_mzXML_201106211454.tar.gz" this dataset on > my machine. But when I have used "PAe000030_mzXML_201104131929.tar.gz", I > got error. Here's the complete command and sessioninfo. > > library(xcms) > > files <- list.files("PAe000030",recursive=TRUE,full.names=TRUE) > files > [1] "PAe000030/hui_serum10_full.mzXML" > [2] "PAe000030/hui_serum16_full.mzXML" > [3] "PAe000030/hui_serum17_full.mzXML" > [4] "PAe000030/hui_serum18_full.mzXML" > . >> xr<-xcmsRaw(files[1]) > Warning message: > In `profStep<-`(`*tmp*`, value = 1) : > MS1 scans empty. Skipping profile matrix calculation. Investigating the content of the files sheds some light on the source of the error. None of the 64 files has any MS1 spectra - they only contain MS2 spectra. The observed result seems thus to be correct. >> xr<-xcmsRaw(files) > Error in file(con, "rb") : invalid 'description' argument > In addition: Warning message: > In if (!file.exists(filename)) return(FALSE) : > the condition has length > 1 and only the first element will be used Based on ?xcmsRaw, this is not supposed to work - xcmsRaw that a single file as input, as stated by the warning. >> xr <- xcmsSet(files) > Error in x[1]:x[2] : NA/NaN argument Same explanation as above, I assume. Hope this helps. Best wishes, Laurent >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] xcms_1.36.0 Biobase_2.20.1 BiocGenerics_0.6.0 mzR_1.6.2 > [5] Rcpp_0.10.4 > > loaded via a namespace (and not attached): > [1] codetools_0.2-8 > > Kind Regards > > > > On Tue, Aug 6, 2013 at 3:23 PM, Laurent Gatto <lg390 at="" cam.ac.uk=""> wrote: >> >> Dear Reema, >> >> On 6 August 2013 10:22, Reema Singh <reema28sep at="" gmail.com=""> wrote: >> > Dear All, >> > >> > I am trying to import .mzXML files using XCMS package. I have tried it >> > with >> > two different data set ( >> > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe000030 ) and >> > >> > ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/PAe0000<ft p:="" ftp.peptideatlas.org="" pub="" peptideatlas="" repository="" pae000030="">02). >> > After extracting .mzXML files, when i tried to import them using XCMS, >> > I >> > got this output. >> > *PAe000002* >> > files <- list.files("TEST", recursive=TRUE,full.names=TRUE) >> >> xr<-xcmsRaw(files[1]) >> >> xr >> > An "xcmsRaw" object with 2070 mass spectra >> > >> > Time range: 120-5879.1 seconds (2-98 minutes) >> > Mass range: 400.0667-1399.9995 m/z >> > Intensity range: 1-465033000 >> > >> > MSn data on 0 mass(es) >> > with 0 MSn spectra >> > Profile method: bin >> > Profile step: 1 m/z (1001 grid points from 400 to 1400 m/z) >> > >> > Memory usage: 34.4 MB >> > >> > *PAe000030* >> > >> >> files1 <- list.files("TEST1", recursive=TRUE,full.names=TRUE) >> >> xr1<-xcmsRaw(files1[1]) >> > Warning message: >> > In `profStep<-`(`*tmp*`, value = 1) : >> > MS1 scans empty. Skipping profile matrix calculation. >> >> xr1 >> > An "xcmsRaw" object with 0 mass spectra >> > >> > MSn data on 0 mass(es) >> > with 0 MSn spectra >> > Profile method: bin >> > Profile step: no profile data >> > >> > Memory usage: 0.00481 MB >> >> >> > >> > Now My question is Why One dataset is successfulyy imported, whereas in >> > the >> > same dataset got some warnings and datset with zero masses?. >> > >> > I would appreciate any help. >> >> First, we do not know exactly what files you are using for your test. >> Reading all of the PAe000030 mzXML files works well on my computer, >> indicating that it is likely not a mzXML issue as such. >> >> As the warning message suggests, the MS1 scans of that particular >> mzXML file are empty, which terminates the processing. Have you had >> more luck with another file from that experiment? You might want to >> check the offending mzXML file - it might indeed be valid yet 'empty'. >> >> Hope this helps, >> >> Laurent >> >> > Kind Regards >> > >> > >> > -- >> > Reema Singh >> > PhD Scholar >> > Computational Biology and Bioinformatics >> > School of Computational and Integrative Sciences >> > Jawaharlal Nehru University >> > New Delhi-110067 >> > INDIA >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Laurent Gatto >> - http://proteome.sysbiol.cam.ac.uk/lgatto/ >> Cambridge Centre for Proteomics >> - http://www.bio.cam.ac.uk/proteomics >> Using R/Bioconductor for proteomics data analysis >> - http://lgatto.github.io/RforProteomics/ > > > > > -- > Reema Singh > PhD Scholar > Computational Biology and Bioinformatics > School of Computational and Integrative Sciences > Jawaharlal Nehru University > New Delhi-110067 > INDIA -- Laurent Gatto - http://proteome.sysbiol.cam.ac.uk/lgatto/ Cambridge Centre for Proteomics - http://www.bio.cam.ac.uk/proteomics Using R/Bioconductor for proteomics data analysis - http://lgatto.github.io/RforProteomics/ ------------------------------ Message: 5 Date: Tue, 6 Aug 2013 17:32:18 +0200 From: Wolfgang Huber <whuber@embl.de> To: Alexey Moskalev <amoskalev at="" list.ru=""> Cc: bioconductor at r-project.org Subject: Re: [BioC] request Message-ID: <d2f657c9-bc8f-4cce-a176-755c7eada9b9 at="" embl.de=""> Content-Type: text/plain; charset=us-ascii Dear Alexey please type "plotPCA" into the R command line to see how the function computes the PCA, then have a look at the manual page of the functions "prcomp" and "screeplot". @all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value. Best wishes Wolfgang On 6 Aug 2013, at 08:54, Alexey Moskalev <amoskalev at="" list.ru=""> wrote: > I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq? > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Message: 6 Date: Tue, 06 Aug 2013 08:43:43 -0700 From: Valerie Obenchain <vobencha@fhcrc.org> To: Reema Singh <reema28sep at="" gmail.com=""> Cc: bioconductor <bioconductor at="" r-project.org=""> Subject: Re: [BioC] RNASeq:- getting Zero Count Message-ID: <520119AF.1070201 at fhcrc.org> Content-Type: text/plain; charset=windows-1252; format=flowed I would do some investigating with a single bam file. Confirm 'gnModel' and 'aln' have some common seqlevels. This call should produce a result. intersect(seqlevels(aln), seqlevels(gnModel)) Call countOverlaps on a single file. co <- countOverlaps(aln, gnModel) Evidently you only want the bam records that have exactly 5 hits. This could be limiting. To see the distribution of hits make a table of the counts. table(co) Valerie On 08/05/2013 10:05 PM, Reema Singh wrote: > Hi Valerie, > > Thank you so much for the reply. > > After checking the seqlevels, I am able to get rid off the error, but > still getting the zero count entries. Is there any another way of doing > this? > > KInd Regards > > > On Mon, Aug 5, 2013 at 9:21 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> <mailto:vobencha at="" fhcrc.org="">> wrote: > > Hi Reema, > > To perform overlap or matching operations the seqlevels (chromosome > names) of the objects must match. The error message is telling you > that some of these do not match. It's reasonable that a few names > may not match (maybe a chromosome is present in one object and not > the other) but the majority should. > > Check the seqlevels: > seqlevels(aln) > seqlevels(gnModel) > > Which names are common to both: > intersect(seqlevels(gnModel), seqlevels(aln)) > > You can rename seqlevels in several different ways. See > ?renameSeqlevels or ?seqlevels for examples. > > Valerie > > > On 08/04/2013 06:35 AM, Reema Singh wrote: > > Dear All, > > I am trying to extract the read count from three .bam files. But > I am > getting Zero count entries. > > I am using Mycobacterium Tuberculosis H37Rv gtf file ( > ftp://ftp.ensemblgenomes.org/__pub/release-19/bacteria//gtf/ __bacteria_1_collection/__mycobacterium_tuberculosis___h37rv/Mycobacte rium___tuberculosis_h37rv.GCA___000277735.1.19.gtf.gz > <ftp: ftp.ensemblgenomes.org="" pub="" release-19="" bacteria="" gtf="" b="" acteria_1_collection="" mycobacterium_tuberculosis_h37rv="" mycobacterium_tu="" berculosis_h37rv.gca_000277735.1.19.gtf.gz="">) > and RNASeq data used here were downloaded from ( > http://www.ncbi.nlm.nih.gov/__geo/query/acc.cgi?acc=GSE40846 > <http: www.ncbi.nlm.nih.gov="" geo="" query="" acc.cgi?acc="GSE40846">__) > and aligned > with bowtie2. > > > library(GenomicFeatures) > txdb <- > makeTranscriptDbFromGFF(file="__Mycobacterium_tuberculosis__ _h37rv.GCA_000277735.1.19.gtf",__format="gtf") > saveDb(txdb,file="__MycoTubeH37Rv.sqlite") > load("MycoTubeH37Rv.sqlite") > gnModel <- exonsBy(txdb,"gene") ### *also tried with > "transcripts", "cds", > but getting same * > > > bamFiles <- list.files(".", "bam$", full=TRUE) > names(bamFiles) <- sub("\\..*","",basename(__bamFiles)) > counter <- function(fl, gnModel){ > aln <- GenomicRanges::__readGappedAlignments(fl) > strand(aln) > hits <- countOverlaps(aln,gnModel) > counts <- countOverlaps(gnModel,aln[__hits==5]) > names(counts) <- names(gnModel) > counts > } > > counts <- sapply(bamFiles,counter,__gnModel) > > Note: method with signature ?Vector#GRangesList? chosen for function > ?countOverlaps?, > target signature ?GappedAlignments#GRangesList?__. > "GappedAlignments#Vector" would also be valid > Note: method with signature ?GRangesList#Vector? chosen for function > ?countOverlaps?, > target signature ?GRangesList#GappedAlignments?__. > "Vector#GappedAlignments" would also be valid > Warning messages: > 1: In .Seqinfo.mergexy(x, y) : > Each of the 2 combined objects has sequence levels not in > the other: > - in 'x': gi|448814763|ref|NC_000962.3| > - in 'y': Chromosome > Make sure to always combine/compare objects based on the > same reference > genome (use suppressWarnings() to suppress this warning). > 2: In .Seqinfo.mergexy(x, y) : > Each of the 2 combined objects has sequence levels not in > the other: > - in 'x': Chromosome > - in 'y': gi|448814763|ref|NC_000962.3| > Make sure to always combine/compare objects based on the > same reference > genome (use suppressWarnings() to suppress this warning). > 3: In .Seqinfo.mergexy(x, y) : > Each of the 2 combined objects has sequence levels not in > the other: > - in 'x': gi|448814763|ref|NC_000962.3| > - in 'y': Chromosome > Make sure to always combine/compare objects based on the > same reference > genome (use suppressWarnings() to suppress this warning). > 4: In .Seqinfo.mergexy(x, y) : > Each of the 2 combined objects has sequence levels not in > the other: > - in 'x': Chromosome > - in 'y': gi|448814763|ref|NC_000962.3| > Make sure to always combine/compare objects based on the > same reference > genome (use suppressWarnings() to suppress this warning). > 5: In .Seqinfo.mergexy(x, y) : > Each of the 2 combined objects has sequence levels not in > the other: > - in 'x': gi|448814763|ref|NC_000962.3| > - in 'y': Chromosome > Make sure to always combine/compare objects based on the > same reference > genome (use suppressWarnings() to suppress this warning). > 6: In .Seqinfo.mergexy(x, y) : > Each of the 2 combined objects has sequence levels not in > the other: > - in 'x': Chromosome > - in 'y': gi|448814763|ref|NC_000962.3| > Make sure to always combine/compare objects based on the > same reference > genome (use suppressWarnings() to suppress this warning). > > head(counts) > > SRR568038 SRR568039 SRR568040 > RVBD_0001 0 0 0 > RVBD_0002 0 0 0 > RVBD_0003 0 0 0 > RVBD_0004 0 0 0 > RVBD_0005 0 0 0 > RVBD_0006 0 0 0 > > sessionInfo() > > R version 3.0.1 (2013-05-16) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] Rsamtools_1.12.3 Biostrings_2.28.0 > GenomicFeatures_1.12.3 > [4] AnnotationDbi_1.22.6 Biobase_2.20.1 > GenomicRanges_1.12.4 > [7] IRanges_1.18.2 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.16.0 bitops_1.0-5 BSgenome_1.28.0 > DBI_0.2-6 > > [5] RCurl_1.95-4.1 RSQLite_0.11.3 rtracklayer_1.20.4 > stats4_3.0.1 > > [9] tools_3.0.1 XML_3.96-1.1 zlibbioc_1.6.0 > > > Kind regards > > > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > Reema Singh > PhD Scholar > Computational Biology and Bioinformatics > School of Computational and Integrative Sciences > Jawaharlal Nehru University > New Delhi-110067 > INDIA ------------------------------ Message: 7 Date: Tue, 6 Aug 2013 11:48:57 -0400 From: Patrick Schorderet <patrick.schorderet@molbio.mgh.harvard.edu> To: bioconductor at r-project.org Subject: [BioC] Extracting overlapping gene names from a list of peaks Message-ID: <56CB5B3C-0D88-4A16-8D4D-3A3B9F0ED3FD at molbio.mgh.harvard.edu> Content-Type: text/plain Dear all, I have a list of peaks from ChIPseq experiments. Now I am trying to find to over which genes these peaks overlap (and extract the gene name). I'm sure this should be pretty easy, but I am just starting with bioconductor, so some concepts are still vague. Here's what I did so far: # Not run because it is installed (as well as other packages) # source("http://bioconductor.org/biocLite.R") # biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene") # Load the Dmelanogaster genome library(TxDb.Dmelanogaster.UCSC.dm3.ensGene, quietly = TRUE) txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene ee <- exonsBy(txdb, "gene") # Load an subset of my peaks for the sake of the example finalPeaks <- rbind(c("chr3R", "2788500", "2842850", "2815675", "54350"), (c("chr3R", "12484350", "12661350", "12572850", "177000"))) rownames(finalPeaks) <- c("Peak 1", "Peak 2") colnames(finalPeaks) <- c("chr", "start", "end", "center", "length") # Create a GRanges object with the file I have # finalPeaks is a matrix with rows being individual peaks and columns <- c() GRfinalPeaks <- GRanges(finalPeaks[,1], IRanges(start = as.numeric(finalPeaks[,2]), end = as.numeric(finalPeaks[,3]))) I'm stuck from here. What I'd like is to get, for each peak, the overlapping genes. For example, an output that would be: Peak1: GeneA, GeneB, GeneC, etc Peak2: GeneD Also, I don't know how simple it is because (as specified in the output example) one peak can overlap several genes or none at all.. Thanks for any help, Patrick [[alternative HTML version deleted]] ------------------------------ Message: 8 Date: Tue, 6 Aug 2013 09:12:05 -0700 (PDT) From: "Bernard North [guest]" <guest@bioconductor.org> To: bioconductor at r-project.org, b.v.north at qmul.ac.uk Cc: CGHcall Maintainer <mark.vdwiel at="" vumc.nl=""> Subject: [BioC] CGHCall problems Message-ID: <20130806161205.C269B143590 at mamba.fhcrc.org> Dear All, I am using CGHcall to segment and call aCGH copy number data. My understanding is that the segmentation step of CGHcall is the same CBS method used in DNAcopy. CGHcall has a function called "calls" which has segments as rows (defined as start probe to end probe) and columns for each sample with the elements being calls. Given that DNAcopy has a different segmentation for each sample how is the segmentation in allcalls decided upon ? Calls is run as allcalls<-data.frame(calls(result)) where result is the final CGHCall object as per the vignette Also does CGHcall provide pvalues or qvalues to test if any regions are recurrently amplified or deleted over samples ? -- output of sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] CGHcall_2.18.0 snowfall_1.84-4 snow_0.3-12 CGHbase_1.18.0 [5] marray_1.36.0 impute_1.32.0 GEOquery_2.24.1 Biobase_2.18.0 [9] BiocGenerics_0.4.0 snapCGH_1.28.0 limma_3.14.4 DNAcopy_1.32.0 loaded via a namespace (and not attached): [1] aCGH_1.36.0 affy_1.36.1 affyio_1.26.0 [4] annotate_1.36.0 AnnotationDbi_1.20.7 BiocInstaller_1.8.3 [7] cluster_1.14.3 DBI_0.2-7 genefilter_1.40.0 [10] GLAD_2.20.0 grid_2.15.2 IRanges_1.16.6 [13] lattice_0.20-10 MASS_7.3-22 multtest_2.14.0 [16] parallel_2.15.2 pixmap_0.4-11 preprocessCore_1.20.0 [19] RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4 [22] splines_2.15.2 stats4_2.15.2 strucchange_1.4-7 [25] survival_2.36-14 tilingArray_1.36.0 vsn_3.26.0 [28] XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.4.0 > -- Sent via the guest posting facility at bioconductor.org. ------------------------------ Message: 9 Date: Tue, 06 Aug 2013 12:14:49 -0400 From: "James W. MacDonald" <jmacdon@uw.edu> To: Patrick Schorderet <patrick.schorderet at="" molbio.mgh.harvard.edu=""> Cc: bioconductor at r-project.org Subject: Re: [BioC] Extracting overlapping gene names from a list of peaks Message-ID: <520120F9.50600 at uw.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Patrick, On 8/6/2013 11:48 AM, Patrick Schorderet wrote: > Dear all, > > I have a list of peaks from ChIPseq experiments. Now I am trying to find to over which genes these peaks overlap (and extract the gene name). > I'm sure this should be pretty easy, but I am just starting with bioconductor, so some concepts are still vague. > Here's what I did so far: > > # Not run because it is installed (as well as other packages) > # source("http://bioconductor.org/biocLite.R") > # biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene") > # Load the Dmelanogaster genome > library(TxDb.Dmelanogaster.UCSC.dm3.ensGene, quietly = TRUE) > txdb<- TxDb.Dmelanogaster.UCSC.dm3.ensGene > ee<- exonsBy(txdb, "gene") > > # Load an subset of my peaks for the sake of the example > finalPeaks<- rbind(c("chr3R", "2788500", "2842850", "2815675", "54350"), (c("chr3R", "12484350", "12661350", "12572850", "177000"))) > rownames(finalPeaks)<- c("Peak 1", "Peak 2") > colnames(finalPeaks)<- c("chr", "start", "end", "center", "length") > > # Create a GRanges object with the file I have > # finalPeaks is a matrix with rows being individual peaks and columns<- c() > GRfinalPeaks<- GRanges(finalPeaks[,1], IRanges(start = as.numeric(finalPeaks[,2]), end = as.numeric(finalPeaks[,3]))) > > I'm stuck from here. What I'd like is to get, for each peak, the overlapping genes. > For example, an output that would be: > > Peak1: GeneA, GeneB, GeneC, etc > Peak2: GeneD > > Also, I don't know how simple it is because (as specified in the output example) one peak can overlap several genes or none at all.. > Thanks for any help, > sapply(1:2, function(x) names(ee[ee %over% GRfinalPeaks[x,],])) [[1]] [1] "FBgn0260642" [[2]] [1] "FBgn0000014" "FBgn0003944" "FBgn0015230" "FBgn0020556" "FBgn0051498" [6] "FBgn0063261" "FBgn0084245" "FBgn0084688" "FBgn0085056" You can then coerce that to whatever form you like. Best, Jim > > Patrick > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 ------------------------------ Message: 10 Date: Tue, 06 Aug 2013 20:35:20 +0400 From: Alexey Moskalev <amoskalev@list.ru> To: Wolfgang Huber <whuber at="" embl.de=""> Cc: bioconductor at r-project.org Subject: Re: [BioC] request Message-ID: <1375806920.474023715 at f117.i.mail.ru> Content-Type: text/plain Dear??Wolfgang! Greate, it works! Thank you so much! Alex ??????????????, 6 ?????????????? 2013, 17:32 +02:00 ???? Wolfgang Huber <whuber at="" embl.de="">: >Dear Alexey >please type "plotPCA" into the R command line to see how the function computes the PCA, then have a look at the manual page of the functions "prcomp" and "screeplot". > >@all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value. > >Best wishes >Wolfgang > > > >On 6 Aug 2013, at 08:54, Alexey Moskalev < amoskalev at list.ru > wrote: > >> I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq? >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Sincerely, Dr. Alexey Moskalev Head of the Laboratory of Molecular Radiobiology and Gerontology Institute of Biology, Komi Science Center of RAS, Kommunisticheskaya St.28 167982, Syktyvkar Russia Blog: http://aging-genes.livejournal.com/ [[alternative HTML version deleted]] ------------------------------ Message: 11 Date: Tue, 6 Aug 2013 17:12:12 +0000 From: "Taylor, Sean D" <sdtaylor@fhcrc.org> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] DNAStringSetList can't coerce a list? Message-ID: <83AF5F78BA8BF748B81D11EF2FE1C46D05BED6 at adama.fhcrc.org> Content-Type: text/plain Nevermind. I restarted my R session and that seems to have helped. From: Taylor, Sean D Sent: Monday, August 05, 2013 4:59 PM To: bioconductor at r-project.org Cc: Pages, Herve (hpages at fhcrc.org) Subject: RE: DNAStringSetList can't coerce a list? Sorry, here is my sessionInfo() > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.1.0 BiocInstaller_1.11.4 ShortRead_1.19.10 [4] latticeExtra_0.6-24 RColorBrewer_1.0-5 lattice_0.20-15 [7] Rsamtools_1.13.27 Biostrings_2.29.14 GenomicRanges_1.13.35 [10] IRanges_1.19.20 BiocGenerics_0.7.3 magicaxis_1.5 loaded via a namespace (and not attached): [1] Biobase_2.20.0 bitops_1.0-5 grid_3.0.1 hwriter_1.3 stats4_3.0.1 [6] tools_3.0.1 zlibbioc_1.6.0 From: Taylor, Sean D Sent: Monday, August 05, 2013 4:58 PM To: bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> Cc: Pages, Herve (hpages at fhcrc.org<mailto:hpages at="" fhcrc.org="">) Subject: DNAStringSetList can't coerce a list? Hi Herve, It seems like I used to be able to coerce a list of DNA String Sets into a DNAStringSetList. With the latest build though it seems like that is no longer the case: > dna1 <- c("AAA", "AC", "", "T", "GGATA") > dna2 <- c("G", "TT", "C") > foo<-DNAStringSet(dna1) > bar<-DNAStringSet(dna2) > DNAStringSetList(foo, bar) DNAStringSetList of length 2 [[1]] AAA AC T GGATA [[2]] G TT C > baz<-list(foo, bar) > DNAStringSetList(baz) Error in IRanges:::new_XVectorList_from_list_of_XVector(tmp_class, x) : all elements in 'x' must be DNAString objects Thanks, Sean Sean Taylor Post-doctoral Fellow Fred Hutchinson Cancer Research Center 206-667-5544 [[alternative HTML version deleted]] ------------------------------ Message: 12 Date: Tue, 6 Aug 2013 13:52:33 -0400 From: Li Liu <liliu_1@hotmail.com> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Cc: "Rafael A. Irizarry" <rafa at="" jhu.edu=""> Subject: [BioC] fRMA package Message-ID: <bay175-w1e98a7a235246849bda1dd45d0 at="" phx.gbl=""> Content-Type: text/plain Hi, I want to use the rRMA package in the Bioconductor. I can install the package successfully but when I run the library there is and error. Is there anybody who can help? Thanks. Li > biocLite("frma") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'frma' trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/con trib/3.0/frma_1.12.0.zip' Content type 'application/zip' length 262021 bytes (255 Kb) opened URL downloaded 255 Kb package ?frma? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Documents and Settings\li\Local Settings\Temp\RtmpYpJMpj\downloaded_packages > library(frma) Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/Program Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll': LoadLibrary failure: The specified procedure could not be found. Error: package or namespace load failed for ?frma? > sessionInfo() R version 3.0.1 (2013-05-16) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0 [4] tools_3.0.1 zlibbioc_1.6.0 [[alternative HTML version deleted]] ------------------------------ Message: 13 Date: Tue, 6 Aug 2013 11:29:50 -0700 From: Michael Lawrence <lawrence.michael@gene.com> To: Julian Gehring <julian.gehring at="" embl.de=""> Cc: Bioconductor List <bioconductor at="" stat.math.ethz.ch=""> Subject: Re: [BioC] ggbio: Data stored twice in 'GGbio' object Message-ID: <caoq5nycmovhtu5yy2p+gt8tdc6wvp377gjdn0p4atlt1gbfpow at="" mail.gmail.com=""> Content-Type: text/plain This is a flaw in the design of ggbio. It was a solution to the problem of ggplot2 requiring a data.frame in the plot object, while ggbio would like to keep the original data structure (like a GRanges) around. Probably the correct solution is for ggbio to extend the ggplot object, or otherwise represent the plot, and to perform the necessary reduction of the data when the plot is rendered. This is how the ggsubplot package works, although it is not changing the underlying data structure. But the data is only stored *exactly* twice if the input data is a data.frame. It's not very efficient to store the data twice, but my main concern is the redundancy in the data model. On Tue, Aug 6, 2013 at 2:33 AM, Julian Gehring <julian.gehring at="" embl.de="">wrote: > Hi, > > The 'ggbio::ggplot' (ggbio_1.9.7, R_2013-08-05 r63513) function seems to > store its data twice. > > library(ggbio) > df = data.frame(x = 1:10, y = rnorm(10)) > p = ggbio::ggplot(data = df) > str(p) > identical(p at data, p at ggplot$data) ## TRUE > > shows that the data 'df' is stored in p at data as well as p at ggplot$data. > > Especially for large data sets, this is inefficient. Is there a good > reason for this? > > Best wishes > Julian > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]] ------------------------------ Message: 14 Date: Tue, 6 Aug 2013 11:36:53 -0700 From: Dan Tenenbaum <dtenenba@fhcrc.org> To: Li Liu <liliu_1 at="" hotmail.com=""> Cc: "Rafael A. Irizarry" <rafa at="" jhu.edu="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] fRMA package Message-ID: <caf42j23xu7h+darxqndfdc7ssjeb6stovzdhqjafs020a4dkgw at="" mail.gmail.com=""> Content-Type: text/plain; charset=windows-1252 On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: > Hi, > > I want to use the rRMA package in the Bioconductor. I can install the package successfully but when I run the library there is and error. Is there anybody who can help? Thanks. > > Li > > >> biocLite("frma") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. > Installing package(s) 'frma' > trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/c ontrib/3.0/frma_1.12.0.zip' > Content type 'application/zip' length 262021 bytes (255 Kb) > opened URL > downloaded 255 Kb > > package ?frma? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Documents and Settings\li\Local Settings\Temp\RtmpYpJMpj\downloaded_packages > >> library(frma) > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared object 'C:/Program Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll': > LoadLibrary failure: The specified procedure could not be found. > > Error: package or namespace load failed for ?frma? > Are you on windows XP? If I recall correctly, the problem is that affxparser does not always work on Windows XP. More information here: https://stat.ethz.ch/pipermail/bioconductor/2013-March/051760.html Dan >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0 > [4] tools_3.0.1 zlibbioc_1.6.0 > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Message: 15 Date: Tue, 6 Aug 2013 20:33:55 +0100 From: Laurent Gatto <lg390@cam.ac.uk> To: Wolfgang Huber <whuber at="" embl.de=""> Cc: Alexey Moskalev <amoskalev at="" list.ru="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] request Message-ID: <ca+unozhjc56h=wyr-fhm+f1jd2=p4fgrwscqh7od82csj0r8jg at="" mail.gmail.com=""> Content-Type: text/plain; charset=ISO-8859-1 On 6 August 2013 16:32, Wolfgang Huber <whuber at="" embl.de=""> wrote: > @all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value. I have a similar function (pRoloc::plot2D) that invisibly returns the prcomp(...)$x[, dims] matrix that used for plotting, where dims are the PCs requested by the user (default being 1:2). I also report the proportion of variance explained by these two components on the axes. Best wishes, Laurent > Best wishes > Wolfgang > > > > On 6 Aug 2013, at 08:54, Alexey Moskalev <amoskalev at="" list.ru=""> wrote: > >> I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq? >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Laurent Gatto - http://proteome.sysbiol.cam.ac.uk/lgatto/ Cambridge Centre for Proteomics - http://www.bio.cam.ac.uk/proteomics Using R/Bioconductor for proteomics data analysis - http://lgatto.github.io/RforProteomics/ ------------------------------ Message: 16 Date: Tue, 06 Aug 2013 23:35:10 +0400 From: Alexey Moskalev <amoskalev@list.ru> To: Laurent Gatto <lg390 at="" cam.ac.uk=""> Cc: bioconductor at r-project.org <bioconductor at="" r-project.org=""> Subject: Re: [BioC] request Message-ID: <1375817710.455500561 at f406.i.mail.ru> Content-Type: text/plain Thanks a lot! ??????????????, 6 ?????????????? 2013, 20:33 +01:00 ???? Laurent Gatto <lg390 at="" cam.ac.uk="">: >On 6 August 2013 16:32, Wolfgang Huber < whuber at embl.de > wrote: >> @all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value. > >I have a similar function (pRoloc::plot2D) that invisibly returns the >prcomp(...)$x[, dims] matrix that used for plotting, where dims are >the PCs requested by the user (default being 1:2). I also report the >proportion of variance explained by these two components on the axes. > >Best wishes, > >Laurent > >> Best wishes >> Wolfgang >> >> >> >> On 6 Aug 2013, at 08:54, Alexey Moskalev < amoskalev at list.ru > wrote: >> >>> I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq? >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > >-- >Laurent Gatto >- http://proteome.sysbiol.cam.ac.uk/lgatto/ >Cambridge Centre for Proteomics >- http://www.bio.cam.ac.uk/proteomics >Using R/Bioconductor for proteomics data analysis >- http://lgatto.github.io/RforProteomics/ Sincerely, Dr. Alexey Moskalev Head of the Laboratory of Molecular Radiobiology and Gerontology Institute of Biology, Komi Science Center of RAS, Kommunisticheskaya St.28 167982, Syktyvkar Russia Blog: http://aging-genes.livejournal.com/ [[alternative HTML version deleted]] ------------------------------ Message: 17 Date: Tue, 6 Aug 2013 21:49:17 +0200 From: Wolfgang Huber <whuber@embl.de> To: Laurent Gatto <lg390 at="" cam.ac.uk=""> Cc: Alexey Moskalev <amoskalev at="" list.ru="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] request Message-ID: <1737A4C1-55CF-4DFC-9994-389152B59ACA at embl.de> Content-Type: text/plain; charset=iso-8859-1 Dear Laurent in pRoloc::plot2D the plot is a side effect (via graphics::plot), and therefore you are free to return something else; while in the function discussed below the plot (a 'trellis' object) is the return value, which then usually is rendered via 'print.trellis'. (One could stick additional information like the PCA loadings and eigenvalues into the same (S3-)object, initially I thought this was ugly but maybe it's the way to go.) Best wishes Wolfgang On Aug 6, 2013, at 9:33 pm, Laurent Gatto <lg390 at="" cam.ac.uk=""> wrote: > On 6 August 2013 16:32, Wolfgang Huber <whuber at="" embl.de=""> wrote: >> @all: I am not sure what would be a good user interface would be for modifying the "plotPCA" function so that it can return the 'pca' object for user inspection (such as desired by Alexey); currently it returns the 'trelliis' object as its return value. > > I have a similar function (pRoloc::plot2D) that invisibly returns the > prcomp(...)$x[, dims] matrix that used for plotting, where dims are > the PCs requested by the user (default being 1:2). I also report the > proportion of variance explained by these two components on the axes. > > Best wishes, > > Laurent > >> Best wishes >> Wolfgang >> >> >> >> On 6 Aug 2013, at 08:54, Alexey Moskalev <amoskalev at="" list.ru=""> wrote: >> >>> I am using DeSeq package to produce Principal components biplot on variance stabilized data for my RNASeq data. I was wondering if you advice me how to know Proportion of Variance for the first and the second Principal components using DeSeq? >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Laurent Gatto > - http://proteome.sysbiol.cam.ac.uk/lgatto/ > Cambridge Centre for Proteomics > - http://www.bio.cam.ac.uk/proteomics > Using R/Bioconductor for proteomics data analysis > - http://lgatto.github.io/RforProteomics/ ------------------------------ Message: 18 Date: Tue, 6 Aug 2013 12:53:30 -0700 From: Steve Lianoglou <lianoglou.steve@gene.com> To: Wolfgang Huber <whuber at="" embl.de=""> Cc: Alexey Moskalev <amoskalev at="" list.ru="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] request Message-ID: <caha9mcp6is2r4nr-g2zgzgb_k2e0k0wn=cjnlcpht-3uqcxndw at="" mail.gmail.com=""> Content-Type: text/plain; charset=ISO-8859-1 Hi, On Tue, Aug 6, 2013 at 12:49 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Dear Laurent > in pRoloc::plot2D the plot is a side effect (via graphics::plot), and therefore you are free to return something else; while in the function discussed below the plot (a 'trellis' object) is the return value, which then usually is rendered via 'print.trellis'. > > (One could stick additional information like the PCA loadings and eigenvalues into the same (S3-)object, initially I thought this was ugly but maybe it's the way to go.) Along these lines: is it considered "bad form" to just add a "pca" `attr`-ibute to the xyplot object you are returning? eg: plotPCA <- function(...) { ## ... out <- xyplot(PC2 ~ PC1, ...) attr(out, 'pca') <- pca invisible(out) ## or not invisible } -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech ------------------------------ Message: 19 Date: Tue, 6 Aug 2013 13:13:59 -0700 From: Michael Lawrence <lawrence.michael@gene.com> To: "Cook, Malcolm" <mec at="" stowers.org=""> Cc: Michael Lawrence <lawrence.michael at="" gene.com="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] ggbio facet_gr example sought Message-ID: <caoq5nydotcrp_x4vauinu1boypzzmdn-nte58cuuxdgpxpxbea at="" mail.gmail.com=""> Content-Type: text/plain I'm pretty sure that you can just pass a GRanges to the facets argument, but I haven't tried it. On Sun, Aug 4, 2013 at 4:50 PM, Cook, Malcolm <mec at="" stowers.org=""> wrote: > Hi, > I am unable to find any examples of facet_gr argument to autoplot. > > It is mentioned in > http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio.pdf on > page 9 as: > > Sometime, we need to view different regions, so we also have a facet_gr > argument which > accept a GRanges. If this is provided, it will override the default > seqnames and use provided > region to facet the graphics, this might be useful for different gene > centric views. > > > However there is no further example of its use, and it does not appear in > the list of formals, and it does not appear at all in > http://bioconductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc/ ggbio.pdf > > And the only google hits suggest this feature is out deprecated. > > Am I missing something? > > Is there a contemporary equivalent? Is there some way to facet on > genomic range? Any examples out there? > > Thanks, > > ~ malcolm_cook at stowers.org > [[alternative HTML version deleted]] ------------------------------ Message: 20 Date: Tue, 6 Aug 2013 22:19:24 +0200 From: Julian Gehring <julian.gehring@embl.de> To: Michael Lawrence <lawrence.michael at="" gene.com=""> Cc: Bioconductor List <bioconductor at="" stat.math.ethz.ch=""> Subject: Re: [BioC] ggbio: Data stored twice in 'GGbio' object Message-ID: <52015A4C.8050603 at embl.de> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Hi Michael, I agree that the main problem is that the data is practically stored twice, irrespective whether this is done in the form of two identical or similar object. Especially having the large amounts of genomic data in mind, this way of handling data may not scale well. Best wishes Julian On 08/06/2013 08:29 PM, Michael Lawrence wrote: > This is a flaw in the design of ggbio. It was a solution to the problem of > ggplot2 requiring a data.frame in the plot object, while ggbio would like > to keep the original data structure (like a GRanges) around. Probably the > correct solution is for ggbio to extend the ggplot object, or otherwise > represent the plot, and to perform the necessary reduction of the data when > the plot is rendered. This is how the ggsubplot package works, although it > is not changing the underlying data structure. > > But the data is only stored *exactly* twice if the input data is a > data.frame. It's not very efficient to store the data twice, but my main > concern is the redundancy in the data model. > > > > > On Tue, Aug 6, 2013 at 2:33 AM, Julian Gehring <julian.gehring at="" embl.de="">wrote: > >> Hi, >> >> The 'ggbio::ggplot' (ggbio_1.9.7, R_2013-08-05 r63513) function seems to >> store its data twice. >> >> library(ggbio) >> df = data.frame(x = 1:10, y = rnorm(10)) >> p = ggbio::ggplot(data = df) >> str(p) >> identical(p at data, p at ggplot$data) ## TRUE >> >> shows that the data 'df' is stored in p at data as well as p at ggplot$data. >> >> Especially for large data sets, this is inefficient. Is there a good >> reason for this? >> >> Best wishes >> Julian >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > ------------------------------ Message: 21 Date: Tue, 6 Aug 2013 18:56:51 -0400 From: Li Liu <liliu_1@hotmail.com> To: Dan Tenenbaum <dtenenba at="" fhcrc.org=""> Cc: "rafa at jhu.edu" <rafa at="" jhu.edu="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] fRMA package Message-ID: <bay175-w24939543f62b119aaf3cabd45d0 at="" phx.gbl=""> Content-Type: text/plain Hi Dan, Thank you for the information. I tried to install the package in another computer with windows 7 but it still doesn't work. Is there any other idea? Thanks. Li > Date: Tue, 6 Aug 2013 11:36:53 -0700 > Subject: Re: [BioC] fRMA package > From: dtenenba at fhcrc.org > To: liliu_1 at hotmail.com > CC: bioconductor at r-project.org; rafa at jhu.edu > > On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: > > Hi, > > > > I want to use the rRMA package in the Bioconductor. I can install the package successfully but when I run the library there is and error. Is there anybody who can help? Thanks. > > > > Li > > > > > >> biocLite("frma") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. > > Installing package(s) 'frma' > > trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows /contrib/3.0/frma_1.12.0.zip' > > Content type 'application/zip' length 262021 bytes (255 Kb) > > opened URL > > downloaded 255 Kb > > > > package ?frma? successfully unpacked and MD5 sums checked > > > > The downloaded binary packages are in > > C:\Documents and Settings\li\Local Settings\Temp\RtmpYpJMpj\downloaded_packages > > > >> library(frma) > > Error in inDL(x, as.logical(local), as.logical(now), ...) : > > unable to load shared object 'C:/Program Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll': > > LoadLibrary failure: The specified procedure could not be found. > > > > Error: package or namespace load failed for ?frma? > > > > Are you on windows XP? If I recall correctly, the problem is that > affxparser does not always work on Windows XP. More information here: > > https://stat.ethz.ch/pipermail/bioconductor/2013-March/051760.html > > Dan > > > >> sessionInfo() > > R version 3.0.1 (2013-05-16) > > Platform: i386-w64-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0 > > [4] tools_3.0.1 zlibbioc_1.6.0 > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] ------------------------------ Message: 22 Date: Tue, 6 Aug 2013 15:59:16 -0700 From: Dan Tenenbaum <dtenenba@fhcrc.org> To: Li Liu <liliu_1 at="" hotmail.com=""> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org="">, "rafa at jhu.edu" <rafa at="" jhu.edu=""> Subject: Re: [BioC] fRMA package Message-ID: <caf42j21gw-zbdhtwbffsns9_jjb8pry-nxfbgzztmwmobfbbaq at="" mail.gmail.com=""> Content-Type: text/plain; charset=windows-1252 On Tue, Aug 6, 2013 at 3:56 PM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: > Hi Dan, > > Thank you for the information. I tried to install the package in another > computer with windows 7 but it still doesn't work. Is there any other idea? > Can you send the exact commands you tried and R's response? Also the output of sessionInfo(). Thanks, Dan > Thanks. > > Li > >> Date: Tue, 6 Aug 2013 11:36:53 -0700 >> Subject: Re: [BioC] fRMA package >> From: dtenenba at fhcrc.org >> To: liliu_1 at hotmail.com >> CC: bioconductor at r-project.org; rafa at jhu.edu >> >> On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: >> > Hi, >> > >> > I want to use the rRMA package in the Bioconductor. I can install the >> > package successfully but when I run the library there is and error. Is there >> > anybody who can help? Thanks. >> > >> > Li >> > >> > >> >> biocLite("frma") >> > BioC_mirror: http://bioconductor.org >> > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. >> > Installing package(s) 'frma' >> > trying URL >> > 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3 .0/frma_1.12.0.zip' >> > Content type 'application/zip' length 262021 bytes (255 Kb) >> > opened URL >> > downloaded 255 Kb >> > >> > package ?frma? successfully unpacked and MD5 sums checked >> > >> > The downloaded binary packages are in >> > C:\Documents and Settings\li\Local >> > Settings\Temp\RtmpYpJMpj\downloaded_packages >> > >> >> library(frma) >> > Error in inDL(x, as.logical(local), as.logical(now), ...) : >> > unable to load shared object 'C:/Program >> > Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll': >> > LoadLibrary failure: The specified procedure could not be found. >> > >> > Error: package or namespace load failed for ?frma? >> > >> >> Are you on windows XP? If I recall correctly, the problem is that >> affxparser does not always work on Windows XP. More information here: >> >> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051760.html >> >> Dan >> >> >> >> sessionInfo() >> > R version 3.0.1 (2013-05-16) >> > Platform: i386-w64-mingw32/i386 (32-bit) >> > >> > locale: >> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> > States.1252 >> > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> > [5] LC_TIME=English_United States.1252 >> > >> > attached base packages: >> > [1] parallel stats graphics grDevices utils datasets methods base >> > >> > other attached packages: >> > [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 >> > >> > loaded via a namespace (and not attached): >> > [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0 >> > [4] tools_3.0.1 zlibbioc_1.6.0 >> > >> > >> > [[alternative HTML version deleted]] >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Message: 23 Date: Tue, 6 Aug 2013 16:47:48 -0700 From: Michael Lawrence <lawrence.michael@gene.com> To: Patrick Schorderet <patrick.schorderet at="" molbio.mgh.harvard.edu=""> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] Extracting overlapping gene names from a list of peaks Message-ID: <caoq5nydnottmzu_p_zthsc9kksxhyy+cgprwds52zdqmrhb1oa at="" mail.gmail.com=""> Content-Type: text/plain You can efficiently get a list like this: hits <- findOverlaps(GRfinalPeaks, ee) listOfGenesByPeak <- split(names(ee)[subjectHits(hits)], queryHits(hits)) But maybe what you want is a long-form table: DataFrame(peak = queryHits(hits), gene = names(ee)[subjectHits(hits)]) On Tue, Aug 6, 2013 at 8:48 AM, Patrick Schorderet < patrick.schorderet at molbio.mgh.harvard.edu> wrote: > Dear all, > > I have a list of peaks from ChIPseq experiments. Now I am trying to find > to over which genes these peaks overlap (and extract the gene name). > I'm sure this should be pretty easy, but I am just starting with > bioconductor, so some concepts are still vague. > Here's what I did so far: > > # Not run because it is installed (as well as other packages) > # source("http://bioconductor.org/biocLite.R") > # biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene") > # Load the Dmelanogaster genome > library(TxDb.Dmelanogaster.UCSC.dm3.ensGene, quietly = TRUE) > txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene > ee <- exonsBy(txdb, "gene") > > # Load an subset of my peaks for the sake of the example > finalPeaks <- rbind(c("chr3R", "2788500", "2842850", "2815675", "54350"), > (c("chr3R", "12484350", "12661350", "12572850", "177000"))) > rownames(finalPeaks) <- c("Peak 1", "Peak 2") > colnames(finalPeaks) <- c("chr", "start", "end", "center", "length") > > # Create a GRanges object with the file I have > # finalPeaks is a matrix with rows being individual peaks and columns <- > c() > GRfinalPeaks <- GRanges(finalPeaks[,1], IRanges(start = > as.numeric(finalPeaks[,2]), end = as.numeric(finalPeaks[,3]))) > > I'm stuck from here. What I'd like is to get, for each peak, the > overlapping genes. > For example, an output that would be: > > Peak1: GeneA, GeneB, GeneC, etc > Peak2: GeneD > > Also, I don't know how simple it is because (as specified in the output > example) one peak can overlap several genes or none at all.. > Thanks for any help, > > Patrick > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] ------------------------------ Message: 24 Date: Tue, 6 Aug 2013 21:55:14 -0400 From: Li Liu <liliu_1@hotmail.com> To: Dan Tenenbaum <dtenenba at="" fhcrc.org=""> Cc: "rafa at jhu.edu" <rafa at="" jhu.edu="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] fRMA package Message-ID: <bay175-w20505596e7e72251ba6acd45e0 at="" phx.gbl=""> Content-Type: text/plain HI Dan, The following is what I run in R studio and the sessionInfo() output in window 7. Thanks. Li > source("http://bioconductor.org/biocLite.R") > biocLite("frma") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'frma' trying URL 'http://bioconductor.org/packages/2.12/bioc/bin/windows/con trib/3.0/frma_1.12.0.zip' Content type 'application/zip' length 262021 bytes (255 Kb) opened URL downloaded 255 Kb package ??rma?successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\lucy\AppData\Local\Temp\Rtmpw3cXZ7\downloaded_packages Warning message: installed directory not writable, cannot update packages 'class', 'foreign', 'MASS', 'mgcv', 'nlme', 'nnet', 'spatial' > library(frma) Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called ??enomicRanges?Error: package or namespace load failed for ??rma? > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 IRanges_1.18.2 [4] MASS_7.3-26 preprocessCore_1.22.0 stats4_3.0.1 [7] tools_3.0.1 zlibbioc_1.6.0 > Date: Tue, 6 Aug 2013 15:59:16 -0700 > Subject: Re: [BioC] fRMA package > From: dtenenba at fhcrc.org > To: liliu_1 at hotmail.com > CC: dtenenba at fhcrc.org; bioconductor at r-project.org; rafa at jhu.edu > > On Tue, Aug 6, 2013 at 3:56 PM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: > > Hi Dan, > > > > Thank you for the information. I tried to install the package in another > > computer with windows 7 but it still doesn't work. Is there any other idea? > > > > Can you send the exact commands you tried and R's response? Also the > output of sessionInfo(). > > Thanks, > Dan > > > > Thanks. > > > > Li > > > >> Date: Tue, 6 Aug 2013 11:36:53 -0700 > >> Subject: Re: [BioC] fRMA package > >> From: dtenenba at fhcrc.org > >> To: liliu_1 at hotmail.com > >> CC: bioconductor at r-project.org; rafa at jhu.edu > >> > >> On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: > >> > Hi, > >> > > >> > I want to use the rRMA package in the Bioconductor. I can install the > >> > package successfully but when I run the library there is and error. Is there > >> > anybody who can help? Thanks. > >> > > >> > Li > >> > > >> > > >> >> biocLite("frma") > >> > BioC_mirror: http://bioconductor.org > >> > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. > >> > Installing package(s) 'frma' > >> > trying URL > >> > 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib /3.0/frma_1.12.0.zip' > >> > Content type 'application/zip' length 262021 bytes (255 Kb) > >> > opened URL > >> > downloaded 255 Kb > >> > > >> > package ??frma?? successfully unpacked and MD5 sums checked > >> > > >> > The downloaded binary packages are in > >> > C:\Documents and Settings\li\Local > >> > Settings\Temp\RtmpYpJMpj\downloaded_packages > >> > > >> >> library(frma) > >> > Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> > unable to load shared object 'C:/Program > >> > Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll': > >> > LoadLibrary failure: The specified procedure could not be found. > >> > > >> > Error: package or namespace load failed for ??frma?? > >> > > >> > >> Are you on windows XP? If I recall correctly, the problem is that > >> affxparser does not always work on Windows XP. More information here: > >> > >> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051760.html > >> > >> Dan > >> > >> > >> >> sessionInfo() > >> > R version 3.0.1 (2013-05-16) > >> > Platform: i386-w64-mingw32/i386 (32-bit) > >> > > >> > locale: > >> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > >> > States.1252 > >> > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > >> > [5] LC_TIME=English_United States.1252 > >> > > >> > attached base packages: > >> > [1] parallel stats graphics grDevices utils datasets methods base > >> > > >> > other attached packages: > >> > [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > >> > > >> > loaded via a namespace (and not attached): > >> > [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0 > >> > [4] tools_3.0.1 zlibbioc_1.6.0 > >> > > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > > >> > _______________________________________________ > >> > Bioconductor mailing list > >> > Bioconductor at r-project.org > >> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > Search the archives: > >> > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] ------------------------------ Message: 25 Date: Tue, 6 Aug 2013 19:31:27 -0700 From: Dan Tenenbaum <dtenenba@fhcrc.org> To: Li Liu <liliu_1 at="" hotmail.com=""> Cc: "rafa at jhu.edu" <rafa at="" jhu.edu="">, "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] fRMA package Message-ID: <caf42j20u3hm=fa=1nqfpcgadc9ywtwiv_pqn2qo8lvox9uzgia at="" mail.gmail.com=""> Content-Type: text/plain; charset=UTF-8 On Tue, Aug 6, 2013 at 6:55 PM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: > HI Dan, > > The following is what I run in R studio and the sessionInfo() output in > window 7. Thanks. > > Li > >> source("http://bioconductor.org/biocLite.R") >> biocLite("frma") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. > Installing package(s) 'frma' > trying URL > 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contrib/3.0/ frma_1.12.0.zip' > Content type 'application/zip' length 262021 bytes (255 Kb) > opened URL > downloaded 255 Kb > > package ?rma?successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\lucy\AppData\Local\Temp\Rtmpw3cXZ7\downloaded_packages > Warning message: > installed directory not writable, cannot update packages 'class', 'foreign', > 'MASS', > 'mgcv', 'nlme', 'nnet', 'spatial' > >> library(frma) > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : > there is no package called ?enomicRanges?Error: package or namespace load > failed for ?rma? > This error is telling you that you need to install GenomicRanges, so: biocLite("GenomicRanges") Then try: library(fRMA) again. Dan >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] affxparser_1.32.3 affyio_1.28.0 IRanges_1.18.2 > [4] MASS_7.3-26 preprocessCore_1.22.0 stats4_3.0.1 > [7] tools_3.0.1 zlibbioc_1.6.0 > > > > > > >> Date: Tue, 6 Aug 2013 15:59:16 -0700 > >> Subject: Re: [BioC] fRMA package >> From: dtenenba at fhcrc.org >> To: liliu_1 at hotmail.com >> CC: dtenenba at fhcrc.org; bioconductor at r-project.org; rafa at jhu.edu > >> >> On Tue, Aug 6, 2013 at 3:56 PM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: >> > Hi Dan, >> > >> > Thank you for the information. I tried to install the package in another >> > computer with windows 7 but it still doesn't work. Is there any other >> > idea? >> > >> >> Can you send the exact commands you tried and R's response? Also the >> output of sessionInfo(). >> >> Thanks, >> Dan >> >> >> > Thanks. >> > >> > Li >> > >> >> Date: Tue, 6 Aug 2013 11:36:53 -0700 >> >> Subject: Re: [BioC] fRMA package >> >> From: dtenenba at fhcrc.org >> >> To: liliu_1 at hotmail.com >> >> CC: bioconductor at r-project.org; rafa at jhu.edu >> >> >> >> On Tue, Aug 6, 2013 at 10:52 AM, Li Liu <liliu_1 at="" hotmail.com=""> wrote: >> >> > Hi, >> >> > >> >> > I want to use the rRMA package in the Bioconductor. I can install the >> >> > package successfully but when I run the library there is and error. >> >> > Is there >> >> > anybody who can help? Thanks. >> >> > >> >> > Li >> >> > >> >> > >> >> >> biocLite("frma") >> >> > BioC_mirror: http://bioconductor.org >> >> > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version >> >> > 3.0.1. >> >> > Installing package(s) 'frma' >> >> > trying URL >> >> > >> >> > 'http://bioconductor.org/packages/2.12/bioc/bin/windows/contri b/3.0/frma_1.12.0.zip' >> >> > Content type 'application/zip' length 262021 bytes (255 Kb) >> >> > opened URL >> >> > downloaded 255 Kb >> >> > >> >> > package ?frma? successfully unpacked and MD5 sums checked >> >> > >> >> > The downloaded binary packages are in >> >> > C:\Documents and Settings\li\Local >> >> > Settings\Temp\RtmpYpJMpj\downloaded_packages >> >> > >> >> >> library(frma) >> >> > Error in inDL(x, as.logical(local), as.logical(now), ...) : >> >> > unable to load shared object 'C:/Program >> >> > Files/R/R-3.0.1/library/affxparser/libs/i386/affxparser.dll': >> >> > LoadLibrary failure: The specified procedure could not be found. >> >> > >> >> > Error: package or namespace load failed for ?frma? >> >> > >> >> >> >> Are you on windows XP? If I recall correctly, the problem is that >> >> affxparser does not always work on Windows XP. More information here: >> >> >> >> https://stat.ethz.ch/pipermail/bioconductor/2013-March/051760.html >> >> >> >> Dan >> >> >> >> >> >> >> sessionInfo() >> >> > R version 3.0.1 (2013-05-16) >> >> > Platform: i386-w64-mingw32/i386 (32-bit) >> >> > >> >> > locale: >> >> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> >> > States.1252 >> >> > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> >> > [5] LC_TIME=English_United States.1252 >> >> > >> >> > attached base packages: >> >> > [1] parallel stats graphics grDevices utils datasets methods base >> >> > >> >> > other attached packages: >> >> > [1] BiocInstaller_1.10.3 affy_1.38.1 Biobase_2.20.1 >> >> > BiocGenerics_0.6.0 >> >> > >> >> > loaded via a namespace (and not attached): >> >> > [1] affyio_1.28.0 MASS_7.3-28 preprocessCore_1.22.0 >> >> > [4] tools_3.0.1 zlibbioc_1.6.0 >> >> > >> >> > >> >> > [[alternative HTML version deleted]] >> >> > >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor at r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Message: 26 Date: Tue, 6 Aug 2013 23:17:39 -0400 From: Tengfei Yin <yintengfei@gmail.com> To: Michael Lawrence <lawrence.michael at="" gene.com=""> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] ggbio facet_gr example sought Message-ID: <capjsq9=gs1qrggoay-n3pfybbhrfjsco40_dfmm3_owbvzr4fg at="" mail.gmail.com=""> Content-Type: text/plain Hi Michael and Malcolm, Sorry for the late reply, that's actually a bug in ggbio now. I did deprecate facet_gr() function, but the feature is kept, it is supposed (used) to work when you pass GRanges to arguments 'facets', either in autoplot() or the low level API. Some of my updates broke this feature. Thanks for pointing this out. I will work on fixing this bug. Tengfei Tengfei On Tue, Aug 6, 2013 at 4:13 PM, Michael Lawrence <lawrence.michael at="" gene.com="">wrote: > I'm pretty sure that you can just pass a GRanges to the facets argument, > but I haven't tried it. > > > On Sun, Aug 4, 2013 at 4:50 PM, Cook, Malcolm <mec at="" stowers.org=""> wrote: > >> Hi, >> I am unable to find any examples of facet_gr argument to autoplot. >> >> It is mentioned in >> http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio. pdfon page 9 as: >> >> Sometime, we need to view different regions, so we also have a facet_gr >> argument which >> accept a GRanges. If this is provided, it will override the default >> seqnames and use provided >> region to facet the graphics, this might be useful for different gene >> centric views. >> >> >> However there is no further example of its use, and it does not appear >> in the list of formals, and it does not appear at all in >> http://bioconductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc /ggbio.pdf >> >> And the only google hits suggest this feature is out deprecated. >> >> Am I missing something? >> >> Is there a contemporary equivalent? Is there some way to facet on >> genomic range? Any examples out there? >> >> Thanks, >> >> ~ malcolm_cook at stowers.org >> > > [[alternative HTML version deleted]] ------------------------------ Message: 27 Date: Tue, 6 Aug 2013 21:02:21 +0800 From: "joseph" <joseph.houjue@gmail.com> To: <bioconductor at="" r-project.org=""> Subject: [BioC] ??: an error in AnnotationForge Message-ID: <001201ce92a5$34c70380$9e550a80$@gmail.com> Content-Type: text/plain Dear Marc Carlson, I??m using AnnotationForge to make my customized package, however, in affymetrix annotation file, some probes correspond to genes have more gene symbols, like this, ??11715100_at?? to ??HIST1H3A /// HIST1H3B /// HIST1H3C /// HIST1H3D /// HIST1H3E /// HIST1H3F /// HIST1H3G /// HIST1H3H /// HIST1H3I /// HIST1H3J??. So that, when I make package: makeDBPackage("HUMANCHIP_DB", affy = TRUE, prefix = "primeview", fileName = "E:/Microarray Data/Affy array database/PrimeView.na33.annot.csv", baseMapType = "ug", version = "1.0.0", manufacturer = "Joseph", chipName = "primeview") Even it works, but this probes could not be matched to expression data, when I annotate it, the output looks like : Gene Symbol 11715100_at 11715100_at 11715104_s_at OTOP2 11715105_at C17orf78 Please tell me how to fix it out. Thanks! Joe [[alternative HTML version deleted]] ------------------------------ Message: 28 Date: Tue, 6 Aug 2013 12:13:48 +0200 From: Nogales Vilardell <cressi.nogales@gmail.com> To: bioconductor at r-project.org Subject: [BioC] beadarray library: perBeadFile Message-ID: <ca+j=4n2wdbdrtsigbfk0paqgdvksfhbf5qvnwxxb4f5=udv23a at="" mail.gmail.com=""> Content-Type: text/plain Hi to everybody, I have started recently to analyse Illumina Bead Chip data. I started without any kind of problem and I was glad with the results until I saw that comment from the beadarray library authors: "iScan come in a different format,.... there are two images of each array section (along with two .locs files), which are labeled Swath1 and Swath2" I don't have those files, I have only the perBeadFile.txt and after the authors wrote: "Given this, simply reading the bead-level text file will result in any function that uses bead locations performing undesirably" And now I am afraid if I did something wrong.. I am not receving any message when I read my files with the function readIllumina and they have also wrote that I should receive a message from the function advising me to use processSwathData. Does anybody know in which cases using perBeadFile.txt is ok and in which cases no? thanks a lot for the help Best wishes Mireia [[alternative HTML version deleted]] ------------------------------ Message: 29 Date: Tue, 6 Aug 2013 21:08:08 +0800 From: "joseph" <joseph.houjue@gmail.com> To: <bioconductor at="" r-project.org=""> Subject: [BioC] ??: an error in AnnotationForge Message-ID: <001f01ce92a6$034282c0$09c78840$@gmail.com> Content-Type: text/plain One more question, if I make this db successfully, when I annotate expression data, there are still some probeID could be annotated with gene symbol, still show ProbeID. However, these probes truly have gene symbol names. How to fix it out? PS. Administrator guy, please approve this mail, maybe we had met before, I worked in SCHARP. Jue Hou,Ph.D. Research Assistant Center of Medical Physics and Technology Hefei Institutes of Physical Science Chinese Academy of Sciences No.350 Shushanhu Road,Shushan District,Heifei,P.R. China Tel. +86551-65595385 Email: <mailto:joseph.houjue at="" gmail.com=""> joseph.houjue at gmail.com; <mailto:houjue00722 at="" sina.com=""> houjue00722 at sina.com ??????: joseph [mailto:joseph.houjue at gmail.com] ????????: 2013??8??4?? 18:35 ??????: bioconductor at r-project.org ????: Re: [BioC] an error in AnnotationForge ??????: ?? Dear Marc Carlson, I??m using AnnotationForge to make my customized package, however, in affymetrix annotation file, some probes correspond to genes have more gene symbols, like this, ??11715100_at?? to ??HIST1H3A /// HIST1H3B /// HIST1H3C /// HIST1H3D /// HIST1H3E /// HIST1H3F /// HIST1H3G /// HIST1H3H /// HIST1H3I /// HIST1H3J??. So that, when I make package: makeDBPackage("HUMANCHIP_DB", affy = TRUE, prefix = "primeview", fileName = "E:/Microarray Data/Affy array database/PrimeView.na33.annot.csv", baseMapType = "ug", version = "1.0.0", manufacturer = "Joseph", chipName = "primeview") Even it works, but this probes could not be matched to expression data, when I annotate it, the output looks like : Gene Symbol 11715100_at 11715100_at 11715104_s_at OTOP2 11715105_at C17orf78 Please tell me how to fix it out. Thanks! Joe [[alternative HTML version deleted]] ------------------------------ Message: 30 Date: Tue, 6 Aug 2013 06:41:05 -0700 From: Datong Wang <datongwang2007@yahoo.com> To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> Subject: [BioC] topGO question Message-ID: <1375796465.32356.YahooMailNeo at web161006.mail.bf1.yahoo.com> Content-Type: text/plain Hi adrian, I used topGO to analyze my data and get the following results: GO.ID Annotated Significant Expected pvalue GO:0016746 123 3 7.13 6.70E-08 GO:0016747 105 3 6.08 6.00E-07 GO:0016757 281 13 16.28 1.50E-05 GO:0016408 15 0 0.87 5.00E-05 GO:0001071 547 32 31.69 7.80E-05 GO:0003700 547 32 31.69 7.80E-05 GO:0046527 89 6 5.16 0.00013 GO:0016759 25 0 1.45 0.00029 GO:0004518 112 1 6.49 0.00062 GO:0016758 209 12 12.11 0.00078 ?? Do you notice 'GO:0016408' and 'GO:0016759'? The number of significant gene of these two GOIDs? is zero. In this case, why they are considered as significant? Can we simply remove them from the list? ? A second question is that : there are many combinations of 'algorithm' and test 'statistics' and the results are not the same and maybe huge different. Which method should we chose for the analysis? datong wang [[alternative HTML version deleted]] ------------------------------ Message: 31 Date: Wed, 7 Aug 2013 08:00:24 +0000 From: "Cook, Malcolm" <mec@stowers.org> To: Tengfei Yin <yintengfei at="" gmail.com="">, Michael Lawrence <lawrence.michael at="" gene.com=""> Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> Subject: Re: [BioC] ggbio facet_gr example sought Message-ID: <d4772401b9d976478c0895769be3e792bc1211 at="" mbsrv02.sgc.loc=""> Content-Type: text/plain Tengfei, Thanks for acknowledging this issue. I played around with this for a while more after Michael's comment, but could find no syntax that did not generate an error. I look forward to learning about this capability once you have it working as you intend. Cheers, ~ malcolm_cook at stowers.org ________________________________ From: Tengfei Yin [yintengfei@gmail.com] Sent: Tuesday, August 06, 2013 10:17 PM To: Michael Lawrence Cc: Cook, Malcolm; bioconductor at r-project.org Subject: Re: ggbio facet_gr example sought Hi Michael and Malcolm, Sorry for the late reply, that's actually a bug in ggbio now. I did deprecate facet_gr() function, but the feature is kept, it is supposed (used) to work when you pass GRanges to arguments 'facets', either in autoplot() or the low level API. Some of my updates broke this feature. Thanks for pointing this out. I will work on fixing this bug. Tengfei Tengfei On Tue, Aug 6, 2013 at 4:13 PM, Michael Lawrence <lawrence.michael at="" gene.com<mailto:lawrence.michael="" at="" gene.com="">> wrote: I'm pretty sure that you can just pass a GRanges to the facets argument, but I haven't tried it. On Sun, Aug 4, 2013 at 4:50 PM, Cook, Malcolm <mec at="" stowers.org<mailto:mec="" at="" stowers.org="">> wrote: Hi, I am unable to find any examples of facet_gr argument to autoplot. It is mentioned in http://bioconductor.org/packages/2.12/bioc/manuals/ggbio/man/ggbio.pdf on page 9 as: Sometime, we need to view different regions, so we also have a facet_gr argument which accept a GRanges. If this is provided, it will override the default seqnames and use provided region to facet the graphics, this might be useful for different gene centric views. However there is no further example of its use, and it does not appear in the list of formals, and it does not appear at all in http://biocon ductor.org/packages/2.12/bioc/vignettes/ggbio/inst/doc/ggbio.pdf And the only google hits suggest this feature is out deprecated. Am I missing something? Is there a contemporary equivalent? Is there some way to facet on genomic range? Any examples out there? Thanks, ~ malcolm_cook at stowers.org<mailto:malcolm_cook at="" stowers.org=""> [[alternative HTML version deleted]] ------------------------------ Message: 32 Date: Wed, 7 Aug 2013 14:56:16 +0530 From: ALok <foralok@gmail.com> To: BioC <bioconductor at="" stat.math.ethz.ch=""> Subject: [BioC] basic query to make groups .. Message-ID: <ca+rrky3nsv+pdfj=ytu6cn2hdkrawgzsupmzpntgsqvqdjdvfg at="" mail.gmail.com=""> Content-Type: text/plain Hi All, Sorry for one basic question. My vector contains two class of group elements, shown in different font and color x=c(*1.1, 1.2, 1.3*, 2.1, 2.2) I am trying to group the objects into two classes, as *1.1, 1.2, 1.3* and 2.1, 2.2 I can use command grep("^1.[12345678910]",x) [1] 1 2 3 > grep("^2.[12345678910]",x) [1] 4 5 but I am not able to automate it, using some variable k. I have many such cases, so I want to write a iterative loop for the structure using some variable k, for test case, lets assume k=1 grep("^k.[12345678910]",x) integer(0) Thanks in advance. Alok -- ************************************************************ Alok Kumar Srivastava Assistant Professor CRRao Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS) Gachibowli, Hyderabad 500046. ************************************************************ [[alternative HTML version deleted]] ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 126, Issue 7 ******************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. 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