ChIPpeakAnno 2.12.2 bug
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Matt, Many thanks for helping us identifying the bug introduced in 2.12.2! The bug has been fixed in version 2.13.1. Please let me know if you have any issues. For future correspondence, could you please keep the discussion in the bioconductor list so others can contribute or benefit? Thanks! Best regards, Julie On 8/13/14 1:18 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at="" fs.fed.us=""> wrote: Hello Julie I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am getting incorrect results from annotatePeakInBatch. More specifically the output column ?insideFeature? is not taking feature strand into account when it is assigning peaks to gene features, the function thinks all gene features are on the positive strand even though my genome ranged data contains strand information. Also all other calculations from annotatePeakInBatch gives the same results as in 2.10. Please let me know if you would like more information about the bug I am getting. Thanks Matt --- Matthew S. Zinkgraf, PhD Postdoctoral Researcher USDA, Forest Service Davis, CA 95618 530-759-1739 mszinkgraf at fs.fed.us <mailto:mszinkgraf at="" fs.fed.us=""> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. [[alternative HTML version deleted]]
ChIPpeakAnno ChIPpeakAnno • 636 views
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@zinkgraf-matthew-s-fs-6703
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Hi Thanks for working on this but I am still getting the same result even with 2.13.1. The annotatePeakInBatch is not assigning peaks to features correctly when genes are located on the negative strand. Below is an example that produces an incorrect result when using annotatePeakInBatch. I think the problem is located in the output= "nearestStart" because "overlapping" produces the correct result. Specifically the second line of the annPeak output should be assigning peak1 to overlapEnd instead of overlapStart because the gene feature is located on the negative strand. Matt > library(ChIPpeakAnno) > > > peak<-RangedData(IRanges(start=as.numeric(as.character(c(1650,2806,8 361))), end=as.numeric(as.character(c(1860,3006,8591)))), space=c("Chr01","Chr01","Chr01"),strand=as.integer(1)) > row.names(peak)<-c("peak1","peak2","peak3") > > > #load subset of data from Populus v210 gff3 file > genome<-as.data.frame(rbind(c("Chr01","phytozome8_0", "gene",1660,2502, ".", "-", ".","Potri.001G000100"),c("Chr01", "phytozome8_0", "gene",2906,6646, ".", "-", ".","Potri.001G000200"),c("Chr01", "phytozome8_0", "gene",8391,8860, ".", "+", ".","Potri.001G000300"))) > > > GENOME<-GFF2RangedData(genome) Warning message: In DataFrame(...) : NAs introduced by coercion > row.names(GENOME)<-genome[,9] > > annPeak = annotatePeakInBatch(peak, AnnotationData=GENOME, PeakLocForDistance ="middle",output="both") Warning messages: 1: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by coercion 2: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by coercion > > View(annPeak) space start end width names peak strand feature start_position end_position insideFeature distancetoFeature shortestDistance Chr01 8361 8591 231 peak3 Potri.001G000300 peak3 + Potri.001G000300 8391 8860 overlapStart 85 30 Chr01 1650 1860 211 peak1 Potri.001G000100 peak1 - Potri.001G000100 1660 2502 overlapStart 747 10 Chr01 2806 3006 201 peak2 Potri.001G000100 peak2 - Potri.001G000100 1660 2502 downstream -404 304 Chr01 2806 3006 201 peak2 Potri.001G000200 peak2 - Potri.001G000200 2906 6646 overlapEnd 3740 100 > > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=C LC_COLLATE=C [5] LC_MONETARY=C LC_MESSAGES=C [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] grid parallel stats graphics grDevices utils [7] datasets methods base other attached packages: [1] ChIPpeakAnno_2.13.1 Biostrings_2.32.1 [3] XVector_0.4.0 IRanges_1.22.10 [5] biomaRt_2.20.0 VennDiagram_1.6.7 [7] GOSemSim_1.22.0 Rcpp_0.11.2 [9] BiocInstaller_1.14.2 edgeR_3.6.7 [11] limma_3.20.8 hash_2.2.6 [13] GSEABase_1.26.0 annotate_1.42.1 [15] GOstats_2.30.0 graph_1.42.0 [17] Category_2.30.0 GO.db_2.14.0 [19] RSQLite_0.11.4 DBI_0.2-7 [21] Matrix_1.1-4 AnnotationDbi_1.26.0 [23] GenomeInfoDb_1.0.2 Biobase_2.24.0 [25] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] AnnotationForge_1.6.1 BBmisc_1.7 [3] BSgenome_1.32.0 BatchJobs_1.3 [5] BiocParallel_0.6.1 GenomicAlignments_1.0.5 [7] GenomicFeatures_1.16.2 GenomicRanges_1.16.4 [9] MASS_7.3-33 RBGL_1.40.0 [11] RCurl_1.95-4.3 Rsamtools_1.16.1 [13] XML_3.98-1.1 bitops_1.0-6 [15] brew_1.0-6 checkmate_1.2 [17] codetools_0.2-8 digest_0.6.4 [19] fail_1.2 foreach_1.4.2 [21] genefilter_1.46.1 iterators_1.0.7 [23] lattice_0.20-29 multtest_2.20.0 [25] rtracklayer_1.24.2 sendmailR_1.1-2 [27] splines_3.1.0 stats4_3.1.0 [29] stringr_0.6.2 survival_2.37-7 [31] tools_3.1.0 xtable_1.7-3 [33] zlibbioc_1.10.0 > From: Zhu, Lihua (Julie) [mailto:Julie.Zhu@umassmed.edu] Sent: Wednesday, August 13, 2014 2:47 PM To: Zinkgraf, Matthew S -FS Cc: bioconductor at r-project.org Subject: Re: ChIPpeakAnno 2.12.2 bug Matt, Many thanks for helping us identifying the bug introduced in 2.12.2! The bug has been fixed in version 2.13.1. Please let me know if you have any issues. For future correspondence, could you please keep the discussion in the bioconductor list so others can contribute or benefit? Thanks! Best regards, Julie On 8/13/14 1:18 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at="" fs.fed.us=""> wrote: Hello Julie I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am getting incorrect results from annotatePeakInBatch. More specifically the output column 'insideFeature' is not taking feature strand into account when it is assigning peaks to gene features, the function thinks all gene features are on the positive strand even though my genome ranged data contains strand information. Also all other calculations from annotatePeakInBatch gives the same results as in 2.10. Please let me know if you would like more information about the bug I am getting. Thanks Matt --- Matthew S. Zinkgraf, PhD Postdoctoral Researcher USDA, Forest Service Davis, CA 95618 530-759-1739 mszinkgraf at fs.fed.us <mailto:mszinkgraf at="" fs.fed.us=""> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. [[alternative HTML version deleted]]
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----- Original Message ----- > From: "Matthew S Zinkgraf -FS" <mszinkgraf at="" fs.fed.us=""> > To: bioconductor at r-project.org > Sent: Monday, August 18, 2014 11:49:07 AM > Subject: Re: [BioC] ChIPpeakAnno 2.12.2 bug > > Hi > > Thanks for working on this but I am still getting the same result > even with 2.13.1. The annotatePeakInBatch is not assigning peaks to > features correctly when genes are located on the negative strand. > Below is an example that produces an incorrect result when using > annotatePeakInBatch. I think the problem is located in the output= > "nearestStart" because "overlapping" produces the correct result. > Specifically the second line of the annPeak output should be > assigning peak1 to overlapEnd instead of overlapStart because the > gene feature is located on the negative strand. > > > > Matt > > > > library(ChIPpeakAnno) > > > > > > peak<-RangedData(IRanges(start=as.numeric(as.character(c(1650,2806 ,8361))), > > end=as.numeric(as.character(c(1860,3006,8591)))), > > space=c("Chr01","Chr01","Chr01"),strand=as.integer(1)) > > row.names(peak)<-c("peak1","peak2","peak3") > > > > > > #load subset of data from Populus v210 gff3 file > > genome<-as.data.frame(rbind(c("Chr01","phytozome8_0", > > "gene",1660,2502, ".", "-", > > ".","Potri.001G000100"),c("Chr01", "phytozome8_0", > > "gene",2906,6646, ".", "-", > > ".","Potri.001G000200"),c("Chr01", "phytozome8_0", > > "gene",8391,8860, ".", "+", ".","Potri.001G000300"))) > > > > > > > GENOME<-GFF2RangedData(genome) > > Warning message: > > In DataFrame(...) : NAs introduced by coercion > > > row.names(GENOME)<-genome[,9] > > > > annPeak = annotatePeakInBatch(peak, AnnotationData=GENOME, > > PeakLocForDistance ="middle",output="both") > Warning messages: > 1: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by > coercion > 2: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by > coercion > > > > View(annPeak) > > space > > start > > end > > width > > names > > peak > > strand > > feature > > start_position > > end_position > > insideFeature > > distancetoFeature > > shortestDistance > > Chr01 > > 8361 > > 8591 > > 231 > > peak3 Potri.001G000300 > > peak3 > > + > > Potri.001G000300 > > 8391 > > 8860 > > overlapStart > > 85 > > 30 > > Chr01 > > 1650 > > 1860 > > 211 > > peak1 Potri.001G000100 > > peak1 > > - > > Potri.001G000100 > > 1660 > > 2502 > > overlapStart > > 747 > > 10 > > Chr01 > > 2806 > > 3006 > > 201 > > peak2 Potri.001G000100 > > peak2 > > - > > Potri.001G000100 > > 1660 > > 2502 > > downstream > > -404 > > 304 > > Chr01 > > 2806 > > 3006 > > 201 > > peak2 Potri.001G000200 > > peak2 > > - > > Potri.001G000200 > > 2906 > > 6646 > > overlapEnd > > 3740 > > 100 > > > > > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=C LC_COLLATE=C > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=C LC_IDENTIFICATION=C > > attached base packages: > [1] grid parallel stats graphics grDevices utils > [7] datasets methods base > > other attached packages: > [1] ChIPpeakAnno_2.13.1 Biostrings_2.32.1 > [3] XVector_0.4.0 IRanges_1.22.10 > [5] biomaRt_2.20.0 VennDiagram_1.6.7 > [7] GOSemSim_1.22.0 Rcpp_0.11.2 > [9] BiocInstaller_1.14.2 edgeR_3.6.7 > [11] limma_3.20.8 hash_2.2.6 > [13] GSEABase_1.26.0 annotate_1.42.1 > [15] GOstats_2.30.0 graph_1.42.0 > [17] Category_2.30.0 GO.db_2.14.0 > [19] RSQLite_0.11.4 DBI_0.2-7 > [21] Matrix_1.1-4 AnnotationDbi_1.26.0 > [23] GenomeInfoDb_1.0.2 Biobase_2.24.0 > [25] BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] AnnotationForge_1.6.1 BBmisc_1.7 > [3] BSgenome_1.32.0 BatchJobs_1.3 > [5] BiocParallel_0.6.1 GenomicAlignments_1.0.5 > [7] GenomicFeatures_1.16.2 GenomicRanges_1.16.4 > [9] MASS_7.3-33 RBGL_1.40.0 > [11] RCurl_1.95-4.3 Rsamtools_1.16.1 > [13] XML_3.98-1.1 bitops_1.0-6 > [15] brew_1.0-6 checkmate_1.2 > [17] codetools_0.2-8 digest_0.6.4 > [19] fail_1.2 foreach_1.4.2 > [21] genefilter_1.46.1 iterators_1.0.7 > [23] lattice_0.20-29 multtest_2.20.0 > [25] rtracklayer_1.24.2 sendmailR_1.1-2 > [27] splines_3.1.0 stats4_3.1.0 > [29] stringr_0.6.2 survival_2.37-7 > [31] tools_3.1.0 xtable_1.7-3 > [33] zlibbioc_1.10.0 > I can't speak about the ChIPpeakAnno issue, but you've installed the devel version of ChIPpeakAnno into an installation that's otherwise using the release version of Bioconductor. This will cause problems all by itself. I suggest either having a separate version of R that runs the devel version, or upgrade your current installation per http://www.bioconductor.org/developers/how-to/useDevel/ . Then see if the problem persists. Dan > > > > > > > > > > From: Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu] > Sent: Wednesday, August 13, 2014 2:47 PM > To: Zinkgraf, Matthew S -FS > Cc: bioconductor at r-project.org > Subject: Re: ChIPpeakAnno 2.12.2 bug > > Matt, > > Many thanks for helping us identifying the bug introduced in 2.12.2! > The bug has been fixed in version 2.13.1. Please let me know if you > have any issues. > > For future correspondence, could you please keep the discussion in > the bioconductor list so others can contribute or benefit? Thanks! > > Best regards, > > Julie > > On 8/13/14 1:18 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at="" fs.fed.us=""> > wrote: > Hello Julie > I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am > getting incorrect results from annotatePeakInBatch. > More specifically the output column 'insideFeature' is not taking > feature strand into account when it is assigning peaks to gene > features, the function thinks all gene features are on the positive > strand even though my genome ranged data contains strand > information. Also all other calculations from annotatePeakInBatch > gives the same results as in 2.10. > > Please let me know if you would like more information about the bug I > am getting. > Thanks > > Matt > > > --- > > Matthew S. Zinkgraf, PhD > Postdoctoral Researcher > USDA, Forest Service > Davis, CA 95618 > 530-759-1739 > mszinkgraf at fs.fed.us <mailto:mszinkgraf at="" fs.fed.us=""> > > > > > > > > This electronic message contains information generated by the USDA > solely for the intended recipients. Any unauthorized interception of > this message or the use or disclosure of the information it contains > may violate the law and subject the violator to civil or criminal > penalties. If you believe you have received this message in error, > please notify the sender and delete the email immediately. > > [[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 >
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 3 days ago
United States
Dear Matt, Thank you again for the report. The bug has been fixed in version 2.12.3. You can check out the new version by svn, svn checkout https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/R packs /ChIPpeakAnno/@93472 path/to/save/ChIPpeakAnno.2.12.3 Please let me know if you have any issues. Yours Sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 8/18/14 2:49 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at="" fs.fed.us=""> wrote: >Hi > >Thanks for working on this but I am still getting the same result even >with 2.13.1. The annotatePeakInBatch is not assigning peaks to features >correctly when genes are located on the negative strand. Below is an >example that produces an incorrect result when using annotatePeakInBatch. >I think the problem is located in the output= "nearestStart" because >"overlapping" produces the correct result. Specifically the second line >of the annPeak output should be assigning peak1 to overlapEnd instead of >overlapStart because the gene feature is located on the negative strand. > > > >Matt > > >> library(ChIPpeakAnno) >> >> >> >>peak<-RangedData(IRanges(start=as.numeric(as.character(c(1650,2806,8 361)) >>), end=as.numeric(as.character(c(1860,3006,8591)))), >>space=c("Chr01","Chr01","Chr01"),strand=as.integer(1)) >> row.names(peak)<-c("peak1","peak2","peak3") >> >> >> #load subset of data from Populus v210 gff3 file >> genome<-as.data.frame(rbind(c("Chr01","phytozome8_0", >>"gene",1660,2502, ".", "-", ".","Potri.001G000100"),c("Chr01", >>"phytozome8_0", "gene",2906,6646, ".", "-", >>".","Potri.001G000200"),c("Chr01", "phytozome8_0", "gene",8391,8860, >>".", "+", ".","Potri.001G000300"))) >> >> > >> GENOME<-GFF2RangedData(genome) > >Warning message: > >In DataFrame(...) : NAs introduced by coercion > >> row.names(GENOME)<-genome[,9] >> >> annPeak = annotatePeakInBatch(peak, AnnotationData=GENOME, >>PeakLocForDistance ="middle",output="both") >Warning messages: >1: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by coercion >2: In mapply(FUN = f, ..., SIMPLIFY = FALSE) : NAs introduced by coercion >> >> View(annPeak) > >space > >start > >end > >width > >names > >peak > >strand > >feature > >start_position > >end_position > >insideFeature > >distancetoFeature > >shortestDistance > >Chr01 > >8361 > >8591 > >231 > >peak3 Potri.001G000300 > >peak3 > >+ > >Potri.001G000300 > >8391 > >8860 > >overlapStart > >85 > >30 > >Chr01 > >1650 > >1860 > >211 > >peak1 Potri.001G000100 > >peak1 > >- > >Potri.001G000100 > >1660 > >2502 > >overlapStart > >747 > >10 > >Chr01 > >2806 > >3006 > >201 > >peak2 Potri.001G000100 > >peak2 > >- > >Potri.001G000100 > >1660 > >2502 > >downstream > >-404 > >304 > >Chr01 > >2806 > >3006 > >201 > >peak2 Potri.001G000200 > >peak2 > >- > >Potri.001G000200 > >2906 > >6646 > >overlapEnd > >3740 > >100 > > > >> >> sessionInfo() >R version 3.1.0 (2014-04-10) >Platform: x86_64-pc-linux-gnu (64-bit) > >locale: >[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=C LC_COLLATE=C > [5] LC_MONETARY=C LC_MESSAGES=C > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C >[11] LC_MEASUREMENT=C LC_IDENTIFICATION=C > >attached base packages: >[1] grid parallel stats graphics grDevices utils >[7] datasets methods base > >other attached packages: >[1] ChIPpeakAnno_2.13.1 Biostrings_2.32.1 > [3] XVector_0.4.0 IRanges_1.22.10 > [5] biomaRt_2.20.0 VennDiagram_1.6.7 > [7] GOSemSim_1.22.0 Rcpp_0.11.2 > [9] BiocInstaller_1.14.2 edgeR_3.6.7 >[11] limma_3.20.8 hash_2.2.6 >[13] GSEABase_1.26.0 annotate_1.42.1 >[15] GOstats_2.30.0 graph_1.42.0 >[17] Category_2.30.0 GO.db_2.14.0 >[19] RSQLite_0.11.4 DBI_0.2-7 >[21] Matrix_1.1-4 AnnotationDbi_1.26.0 >[23] GenomeInfoDb_1.0.2 Biobase_2.24.0 >[25] BiocGenerics_0.10.0 > >loaded via a namespace (and not attached): >[1] AnnotationForge_1.6.1 BBmisc_1.7 > [3] BSgenome_1.32.0 BatchJobs_1.3 > [5] BiocParallel_0.6.1 GenomicAlignments_1.0.5 >[7] GenomicFeatures_1.16.2 GenomicRanges_1.16.4 > [9] MASS_7.3-33 RBGL_1.40.0 >[11] RCurl_1.95-4.3 Rsamtools_1.16.1 >[13] XML_3.98-1.1 bitops_1.0-6 >[15] brew_1.0-6 checkmate_1.2 >[17] codetools_0.2-8 digest_0.6.4 >[19] fail_1.2 foreach_1.4.2 >[21] genefilter_1.46.1 iterators_1.0.7 >[23] lattice_0.20-29 multtest_2.20.0 >[25] rtracklayer_1.24.2 sendmailR_1.1-2 >[27] splines_3.1.0 stats4_3.1.0 >[29] stringr_0.6.2 survival_2.37-7 >[31] tools_3.1.0 xtable_1.7-3 >[33] zlibbioc_1.10.0 > > >> > > > > > > >From: Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu] >Sent: Wednesday, August 13, 2014 2:47 PM >To: Zinkgraf, Matthew S -FS >Cc: bioconductor at r-project.org >Subject: Re: ChIPpeakAnno 2.12.2 bug > >Matt, > >Many thanks for helping us identifying the bug introduced in 2.12.2! The >bug has been fixed in version 2.13.1. Please let me know if you have any >issues. > >For future correspondence, could you please keep the discussion in the >bioconductor list so others can contribute or benefit? Thanks! > >Best regards, > >Julie > >On 8/13/14 1:18 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at="" fs.fed.us=""> >wrote: >Hello Julie >I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am >getting incorrect results from annotatePeakInBatch. >More specifically the output column 'insideFeature' is not taking feature >strand into account when it is assigning peaks to gene features, the >function thinks all gene features are on the positive strand even though >my genome ranged data contains strand information. Also all other >calculations from annotatePeakInBatch gives the same results as in 2.10. > >Please let me know if you would like more information about the bug I am >getting. >Thanks > >Matt > > >--- > >Matthew S. Zinkgraf, PhD >Postdoctoral Researcher >USDA, Forest Service >Davis, CA 95618 >530-759-1739 >mszinkgraf at fs.fed.us <mailto:mszinkgraf at="" fs.fed.us=""> > > > > > > > >This electronic message contains information generated by the USDA solely >for the intended recipients. Any unauthorized interception of this >message or the use or disclosure of the information it contains may >violate the law and subject the violator to civil or criminal penalties. >If you believe you have received this message in error, please notify the >sender and delete the email immediately. > > [[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
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