On 03/14/2014 10:46 AM, Hervé Pagès wrote: > Hi Veerendra, > > Just to let you know that I've fixed the warning you get with > makeTranscriptDbFromGFF() that "the chromosome lengths and > circularity flags are not available for this TranscriptDb object". I mean, I fixed the warning you get with makeTranscriptDbFromBiomart(), not with makeTranscriptDbFromGFF() (which I didn't touch). H. > The fix is in GenomicFeatures 1.14.5 (release) and 1.15.11 (devel), > both of which will become available via biocLite() in the next hour > or so. > > Cheers, > H. > > > On 03/07/2014 03:24 PM, Hervé Pagès wrote: >> Hi Veerendra, >> >> Don't know about the error you get with makeTranscriptDbFromGFF(). >> >> However, please note that you should also be able to create that >> TranscriptDb object thru the Ensembl Mart: >> >> library(GenomicFeatures) >> txdb <- makeTranscriptDbFromBiomart("ensembl", >> "mmusculus_gene_ensembl") >> >> Then: >> >> > txdb >> TranscriptDb object: >> | Db type: TranscriptDb >> | Supporting package: GenomicFeatures >> | Data source: BioMart >> | Organism: Mus musculus >> | Resource URL: www.biomart.org:80 >> | BioMart database: ensembl >> | BioMart database version: ENSEMBL GENES 75 (SANGER UK) >> | BioMart dataset: mmusculus_gene_ensembl >> | BioMart dataset description: Mus musculus genes (GRCm38.p2) >> | BioMart dataset version: GRCm38.p2 >> | Full dataset: yes >> | miRBase build ID: NA >> | transcript_nrow: 94929 >> | exon_nrow: 404385 >> | cds_nrow: 313584 >> | Db created by: GenomicFeatures package from Bioconductor >> | Creation time: 2014-03-07 15:20:13 -0800 (Fri, 07 Mar 2014) >> | GenomicFeatures version at creation time: 1.14.3 >> | RSQLite version at creation time: 0.11.4 >> | DBSCHEMAVERSION: 1.0 >> >> For whatever reason, I got a warning that the chromosome lengths and >> circularity flags are not available for this TranscriptDb object (I'll >> look into this). Not a big deal though, the TranscriptDb object should >> still be fully functional. >> >> Cheers, >> H. >> >> >> On 03/07/2014 01:59 PM, Veerendra Gadekar wrote: >>> Dear Members, >>> >>> Greetings! >>> >>> I am trying to create a Transcript db object, from the GTF file for >>> Musmusculus transcriptome data available at ensembl FTP site >>> >>> (version 75). ftp://ftp.ensembl.org/pub/release-75/gtf/mus_musculus >>> >>> I am using the function, "makeTranscriptDbFromGFF()" from the " >>> GenomicFeatures" bioconductor library. >>> >>> *Command used:* >>> >>>> library("GenomicFeatures") >>>> txdb_75 = makeTranscriptDbFromGFF (file = >>>> '/Mus_musculus.GRCm38.75.gtf', >>> exonRankAttributeName='exon_number', format='gtf', dataSource='ENSEMBL', >>> species='Mus musculus') >>> >>> *Error message:* >>> >>> extracting transcript information >>> Estimating transcript ranges. >>> Error in unique(sub$transcript_id) : >>> error in evaluating the argument 'x' in selecting a method for function >>> 'unique': Error in subs[[i]] : subscript out of bounds >>> >>> I am not able to understand the above error message. However, I could >>> create the transcript db object successfully for the GTF file >>> >>> downloaded from ensembl version 74. >>> ftp://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/ >>> >>> *Session information:* >>> >>>> sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-pc-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=en_US.UTF-8 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 >>> [8] base >>> >>> other attached packages: >>> [1] data.table_1.9.2 biomaRt_2.16.0 GenomicFeatures_1.12.4 >>> [4] AnnotationDbi_1.22.6 Biobase_2.20.1 GenomicRanges_1.12.5 >>> [7] IRanges_1.18.4 BiocGenerics_0.6.0 BiocInstaller_1.10.4 >>> >>> loaded via a namespace (and not attached): >>> [1] Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 DBI_0.2-7 >>> >>> [5] plyr_1.8.1 Rcpp_0.11.0 RCurl_1.95-4.1 >>> reshape2_1.2.2 >>> [9] Rsamtools_1.12.4 RSQLite_0.11.4 rtracklayer_1.20.4 >>> stats4_3.0.2 >>> >>> [13] stringr_0.6.2 tools_3.0.2 XML_3.98-1.1 >>> zlibbioc_1.6.0 >>> >>> Your assistance in this regard would be very much appreciated. >>> >>> Thank you in advance. >>> >>> Best Regards, >>> >>> Veerendra >>> >>> >>> >>> >>> >>> >>> On Wed, Feb 13, 2013 at 1:32 PM, Veerendra GP >>> <gpveerendra09 at="" gmail.com="">wrote: >>> >>>> Dear Valerie, >>>> >>>> Thank you very much for the descriptive reply and your suggestion, it >>>> indeed was a cryptic error for me but now I understand the cause. >>>> >>>> Thanks, >>>> Veerendra >>>> >>>> On Wed, Feb 13, 2013 at 12:19 AM, Valerie Obenchain >>>> <vobencha at="" fhcrc.org="">wrote: >>>> >>>>> Hello, >>>>> >>>>> Thanks for sending a reproducible example. Sorry for the cryptic error >>>>> message. That is something we could improve. >>>>> >>>>> The problem is that for the UCSC data, some transcripts in a single >>>>> gene >>>>> are from different strands. In this case the strand Rle will have >>>>> multiple >>>>> runValues (i.e. runValue longer than 1). >>>>> >>>>> When we summarize strand runValues by elementLength we see the UCSC >>>>> data >>>>> has runValues of 1, 2, 3, 4 and 5. >>>>> >>>>> table(elementLengths(runValue(strand(GenegroupedTranscripts)))) >>>>>> >>>>> >>>>> 1 >>>>> 37315 >>>>> >>>>>> table(elementLengths(runValue(strand(UCSCGenegroupedTranscripts)))) >>>>>> >>>>> >>>>> 1 2 3 4 5 >>>>> 21686 72 1 1 1 >>>>> >>>>> Here is a closer look at the entry that has an elementLength of 3: >>>>> >>>>> UCSC_elts <- elementLengths(runValue(strand( >>>>>> UCSCGenegroupedTranscripts))) >>>>>> UCSCGenegroupedTranscripts[UCSC_elts == 3] >>>>>> >>>>> >>>>> GRangesList of length 1: >>>>> $108816 >>>>> GRanges with 5 ranges and 2 metadata columns: >>>>> seqnames ranges strand | tx_id >>>>> tx_name >>>>> <rle> <iranges> <rle> | <integer> >>>>> <character> >>>>> [1] chr4 [42452733, 42476567] + | 10641 >>>>> uc008smu.1 >>>>> [2] chr4 [42471253, 42471291] + | 10642 >>>>> uc008smv.1 >>>>> [3] chr4 [41902019, 41925853] - | 12216 >>>>> uc008slb.1 >>>>> [4] chr4 [41907295, 41907333] - | 12217 >>>>> uc008slg.1 >>>>> [5] chrUn_random [ 588639, 612480] + | 55359 >>>>> uc012hdn.1 >>>>> >>>>> >>>>> The strand Rle for this gene is, >>>>> >>>>> strand(UCSCGenegroupedTranscripts[UCSC_elts == 3]) >>>>>> >>>>> CompressedRleList of length 1 >>>>> $`108816` >>>>> factor-Rle of length 5 with 3 runs >>>>> Lengths: 2 2 1 >>>>> Values : + - + >>>>> Levels(3): + - * >>>>> >>>>> In the case of multiple stands per list element (per gene in this >>>>> case) >>>>> you can't use as.integer(). It looks like you are after a vector of a >>>>> single strand per gene. Depending on your use case you could remove >>>>> these >>>>> genes or set the strand of these genes to '*'. >>>>> >>>>> >>>>> Valerie >>>>> >>>>> >>>>> >>>>> >>>>> On 02/12/2013 08:11 AM, Veerendra GP wrote: >>>>> >>>>>> Hello Everyone! >>>>>> >>>>>> Greetings! >>>>>> >>>>>> I am using "GenomicFeatures" library to create Transcript db >>>>>> objects for >>>>>> the mouse genome. >>>>>> I did it by using biomart, *makeTranscriptDbFromBiomart()* and also >>>>>> >>>>>> UCSC, makeTranscriptDbFromUCSC() >>>>>> functions. >>>>>> >>>>>> As I am interested in the strand information, I tried fetching the it >>>>>> using >>>>>> *as.integer(),* *runValue**()* & *strand()* functions. I am able to >>>>>> get >>>>>> it >>>>>> from the transcriptdb object, created using >>>>>> *makeTranscriptDbFromBiomart()* but >>>>>> >>>>>> ending up with an error when I am trying to do the same with >>>>>> transcriptdb object created using makeTranscriptDbFromUCSC() >>>>>> function*.* >>>>>> >>>>>> >>>>>> working code: >>>>>> >>>>>> mouseGNM <- makeTranscriptDbFromBiomart (biomart = "ensembl", >>>>>> dataset= >>>>>> "mmusculus_gene_ensembl"); >>>>>> saveDb(mouseGNM, file="MouseGNM.sqlite"); >>>>>> library("GenomicFeatures"); >>>>>> MouseGNM<- loadDb("MouseGNM.sqlite"); >>>>>> GenegroupedTranscripts<- transcriptsBy(MouseGNM, by = "gene"); >>>>>> strand.info <-as.integer(runValue(strand(GenegroupedTranscripts))); >>>>>> >>>>>> runValue(strand(GenegroupedTranscripts)) CompressedIntegerList of >>>>>>> length >>>>>>> >>>>>> 37315 [["ENSMUSG00000000001"]] 2 [["ENSMUSG00000000003"]] 2 >>>>>> [["ENSMUSG00000000028"]] 2 [["ENSMUSG00000000031"]] 2 >>>>>> [["ENSMUSG00000000037"]] 1 [["ENSMUSG00000000049"]] 1 >>>>>> [["ENSMUSG00000000056"]] 1 [["ENSMUSG00000000058"]] 1 >>>>>> [["ENSMUSG00000000078"]] 1 [["ENSMUSG00000000085"]] 1 ... <37305 more >>>>>> elements> >>>>>> >>>>>> strand.info[1:100] >>>>>>> >>>>>> [1] 2 2 2 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 2 1 1 1 2 1 2 1 1 2 2 1 >>>>>> 1 2 1 >>>>>> 2 2 >>>>>> 1 2 [38] 2 1 1 1 1 1 1 2 1 1 2 2 1 1 1 2 2 1 1 1 2 1 2 1 2 2 1 1 1 >>>>>> 1 1 2 >>>>>> 1 >>>>>> 2 2 2 2 [75] 2 2 2 2 2 2 2 1 2 1 1 2 2 2 1 1 1 2 1 2 2 2 1 1 2 1 >>>>>> >>>>>> here 2 is the antisense strand and 1 the sense strand >>>>>> >>>>>> >>>>>> UCSC.mouseGNM <- makeTranscriptDbFromUCSC(genome = "mm9", tablename = >>>>>> "knownGene"); >>>>>> saveDb(UCSC.mouseGNM, file="UCSCMouseGNM.sqlite"); >>>>>> UCSCMouseGNM<- loadDb("UCSCMouseGNM.sqlite"); >>>>>> UCSCGenegroupedTranscripts<- transcriptsBy(UCSCMouseGNM, by = >>>>>> "gene"); >>>>>> strand.info2<- >>>>>> as.integer(runValue(strand(UCSCGenegroupedTranscripts))); >>>>>> >>>>>> runValue(strand(UCSCGenegroupedTranscripts)) >>>>>>> >>>>>> CompressedIntegerList of length 21761 >>>>>> [["100009600"]] 2 >>>>>> [["100009609"]] 2 >>>>>> [["100009614"]] 1 >>>>>> [["100012"]] 2 >>>>>> [["100017"]] 2 >>>>>> [["100019"]] 1 >>>>>> [["100033459"]] 1 >>>>>> [["100034251"]] 1 >>>>>> [["100034361"]] 2 >>>>>> [["100034684"]] 2 >>>>>> ... >>>>>> <21751 more elements> >>>>>> >>>>>> *ERROR:* >>>>>> >>>>>> strand.info2<- as.integer(runValue(strand( >>>>>>> UCSCGenegroupedTranscripts))); >>>>>>> >>>>>> Error in as.vector(x, mode = "integer") : coercing an AtomicList >>>>>> object >>>>>> to >>>>>> an atomic vector is supported only for objects with top-level >>>>>> elements of >>>>>> length <= 1 >>>>>> >>>>>> I am not able to understand this error message, could anyone let me >>>>>> know >>>>>> what is going wrong in the code. >>>>>> Here is the session information. >>>>>> >>>>>> sessionInfo() R version 2.15.2 (2012-10-26) Platform: >>>>>>> x86_64-pc-linux-gnu >>>>>>> >>>>>> (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] >>>>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] >>>>>> LC_MONETARY=en_US.UTF-8 >>>>>> LC_MESSAGES=en_AU.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] GenomicFeatures_1.10.1 >>>>>> AnnotationDbi_1.20.3 >>>>>> Biobase_2.18.0 [4] GenomicRanges_1.10.5 IRanges_1.16.4 >>>>>> BiocGenerics_0.4.0 >>>>>> loaded via a namespace (and not attached): [1] biomaRt_2.14.0 >>>>>> Biostrings_2.26.2 bitops_1.0-5 BSgenome_1.26.1 [5] DBI_0.2-5 >>>>>> parallel_2.15.2 RCurl_1.95-3 Rsamtools_1.10.2 [9] RSQLite_0.11.2 >>>>>> rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 [13] XML_3.95-0.1 >>>>>> zlibbioc_1.4.0 >>>>>> >>>>>> >>>>>> Thank you in advance. >>>>>> Regards, >>>>>> >>>>>> Veerendra. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> GP.Veerendra >>>> PhD Student (Bioinformatics) >>>> Stazione Zoologica Anton Dohrn >>>> Naples, Italy >>>> M:+393663915221 >>>> >>> >>> >>> >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Dear Hervé, Thank you very much for your email. I am going to update my "GenomicFeatures" right now! Just for your information, I tried using "makeTranscriptDbFromBiomart()", as instructed by you in your previous email. It worked fine! Cheers, Veerendra On Fri, Mar 14, 2014 at 6:46 PM, Hervé Pagès <hpages@fhcrc.org> wrote: > Hi Veerendra, > > Just to let you know that I've fixed the warning you get with > makeTranscriptDbFromGFF() that "the chromosome lengths and > circularity flags are not available for this TranscriptDb object". > The fix is in GenomicFeatures 1.14.5 (release) and 1.15.11 (devel), > both of which will become available via biocLite() in the next hour > or so. > > Cheers, > H. > > > > On 03/07/2014 03:24 PM, Hervé Pagès wrote: > >> Hi Veerendra, >> >> Don't know about the error you get with makeTranscriptDbFromGFF(). >> >> However, please note that you should also be able to create that >> TranscriptDb object thru the Ensembl Mart: >> >> library(GenomicFeatures) >> txdb <- makeTranscriptDbFromBiomart("ensembl", >> "mmusculus_gene_ensembl") >> >> Then: >> >> > txdb >> TranscriptDb object: >> | Db type: TranscriptDb >> | Supporting package: GenomicFeatures >> | Data source: BioMart >> | Organism: Mus musculus >> | Resource URL: www.biomart.org:80 >> | BioMart database: ensembl >> | BioMart database version: ENSEMBL GENES 75 (SANGER UK) >> | BioMart dataset: mmusculus_gene_ensembl >> | BioMart dataset description: Mus musculus genes (GRCm38.p2) >> | BioMart dataset version: GRCm38.p2 >> | Full dataset: yes >> | miRBase build ID: NA >> | transcript_nrow: 94929 >> | exon_nrow: 404385 >> | cds_nrow: 313584 >> | Db created by: GenomicFeatures package from Bioconductor >> | Creation time: 2014-03-07 15:20:13 -0800 (Fri, 07 Mar 2014) >> | GenomicFeatures version at creation time: 1.14.3 >> | RSQLite version at creation time: 0.11.4 >> | DBSCHEMAVERSION: 1.0 >> >> For whatever reason, I got a warning that the chromosome lengths and >> circularity flags are not available for this TranscriptDb object (I'll >> look into this). Not a big deal though, the TranscriptDb object should >> still be fully functional. >> >> Cheers, >> H. >> >> >> On 03/07/2014 01:59 PM, Veerendra Gadekar wrote: >> >>> Dear Members, >>> >>> Greetings! >>> >>> I am trying to create a Transcript db object, from the GTF file for >>> Musmusculus transcriptome data available at ensembl FTP site >>> >>> (version 75). ftp://ftp.ensembl.org/pub/release-75/gtf/mus_musculus >>> >>> I am using the function, "makeTranscriptDbFromGFF()" from the " >>> GenomicFeatures" bioconductor library. >>> >>> *Command used:* >>> >>> library("GenomicFeatures") >>>> txdb_75 = makeTranscriptDbFromGFF (file = '/Mus_musculus.GRCm38.75.gtf', >>>> >>> exonRankAttributeName='exon_number', format='gtf', dataSource='ENSEMBL', >>> species='Mus musculus') >>> >>> *Error message:* >>> >>> extracting transcript information >>> Estimating transcript ranges. >>> Error in unique(sub$transcript_id) : >>> error in evaluating the argument 'x' in selecting a method for function >>> 'unique': Error in subs[[i]] : subscript out of bounds >>> >>> I am not able to understand the above error message. However, I could >>> create the transcript db object successfully for the GTF file >>> >>> downloaded from ensembl version 74. >>> ftp://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/ >>> >>> *Session information:* >>> >>> sessionInfo() >>>> >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-pc-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=en_US.UTF-8 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 >>> [8] base >>> >>> other attached packages: >>> [1] data.table_1.9.2 biomaRt_2.16.0 GenomicFeatures_1.12.4 >>> [4] AnnotationDbi_1.22.6 Biobase_2.20.1 GenomicRanges_1.12.5 >>> [7] IRanges_1.18.4 BiocGenerics_0.6.0 BiocInstaller_1.10.4 >>> >>> loaded via a namespace (and not attached): >>> [1] Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 DBI_0.2-7 >>> >>> [5] plyr_1.8.1 Rcpp_0.11.0 RCurl_1.95-4.1 >>> reshape2_1.2.2 >>> [9] Rsamtools_1.12.4 RSQLite_0.11.4 rtracklayer_1.20.4 >>> stats4_3.0.2 >>> >>> [13] stringr_0.6.2 tools_3.0.2 XML_3.98-1.1 >>> zlibbioc_1.6.0 >>> >>> Your assistance in this regard would be very much appreciated. >>> >>> Thank you in advance. >>> >>> Best Regards, >>> >>> Veerendra >>> >>> >>> >>> >>> >>> >>> On Wed, Feb 13, 2013 at 1:32 PM, Veerendra GP >>> <gpveerendra09@gmail.com>wrote: >>> >>> Dear Valerie, >>>> >>>> Thank you very much for the descriptive reply and your suggestion, it >>>> indeed was a cryptic error for me but now I understand the cause. >>>> >>>> Thanks, >>>> Veerendra >>>> >>>> On Wed, Feb 13, 2013 at 12:19 AM, Valerie Obenchain >>>> <vobencha@fhcrc.org>wrote: >>>> >>>> Hello, >>>>> >>>>> Thanks for sending a reproducible example. Sorry for the cryptic error >>>>> message. That is something we could improve. >>>>> >>>>> The problem is that for the UCSC data, some transcripts in a single >>>>> gene >>>>> are from different strands. In this case the strand Rle will have >>>>> multiple >>>>> runValues (i.e. runValue longer than 1). >>>>> >>>>> When we summarize strand runValues by elementLength we see the UCSC >>>>> data >>>>> has runValues of 1, 2, 3, 4 and 5. >>>>> >>>>> table(elementLengths(runValue(strand(GenegroupedTranscripts)))) >>>>> >>>>>> >>>>>> >>>>> 1 >>>>> 37315 >>>>> >>>>> table(elementLengths(runValue(strand(UCSCGenegroupedTranscripts)))) >>>>>> >>>>>> >>>>> 1 2 3 4 5 >>>>> 21686 72 1 1 1 >>>>> >>>>> Here is a closer look at the entry that has an elementLength of 3: >>>>> >>>>> UCSC_elts <- elementLengths(runValue(strand( >>>>> >>>>>> UCSCGenegroupedTranscripts))) >>>>>> UCSCGenegroupedTranscripts[UCSC_elts == 3] >>>>>> >>>>>> >>>>> GRangesList of length 1: >>>>> $108816 >>>>> GRanges with 5 ranges and 2 metadata columns: >>>>> seqnames ranges strand | tx_id tx_name >>>>> <rle> <iranges> <rle> | <integer> <character> >>>>> [1] chr4 [42452733, 42476567] + | 10641 uc008smu.1 >>>>> [2] chr4 [42471253, 42471291] + | 10642 uc008smv.1 >>>>> [3] chr4 [41902019, 41925853] - | 12216 uc008slb.1 >>>>> [4] chr4 [41907295, 41907333] - | 12217 uc008slg.1 >>>>> [5] chrUn_random [ 588639, 612480] + | 55359 uc012hdn.1 >>>>> >>>>> >>>>> The strand Rle for this gene is, >>>>> >>>>> strand(UCSCGenegroupedTranscripts[UCSC_elts == 3]) >>>>> >>>>>> >>>>>> CompressedRleList of length 1 >>>>> $`108816` >>>>> factor-Rle of length 5 with 3 runs >>>>> Lengths: 2 2 1 >>>>> Values : + - + >>>>> Levels(3): + - * >>>>> >>>>> In the case of multiple stands per list element (per gene in this case) >>>>> you can't use as.integer(). It looks like you are after a vector of a >>>>> single strand per gene. Depending on your use case you could remove >>>>> these >>>>> genes or set the strand of these genes to '*'. >>>>> >>>>> >>>>> Valerie >>>>> >>>>> >>>>> >>>>> >>>>> On 02/12/2013 08:11 AM, Veerendra GP wrote: >>>>> >>>>> Hello Everyone! >>>>>> >>>>>> Greetings! >>>>>> >>>>>> I am using "GenomicFeatures" library to create Transcript db >>>>>> objects for >>>>>> the mouse genome. >>>>>> I did it by using biomart, *makeTranscriptDbFromBiomart()* and also >>>>>> >>>>>> UCSC, makeTranscriptDbFromUCSC() >>>>>> functions. >>>>>> >>>>>> As I am interested in the strand information, I tried fetching the it >>>>>> using >>>>>> *as.integer(),* *runValue**()* & *strand()* functions. I am able to >>>>>> get >>>>>> it >>>>>> from the transcriptdb object, created using >>>>>> *makeTranscriptDbFromBiomart()* but >>>>>> >>>>>> ending up with an error when I am trying to do the same with >>>>>> transcriptdb object created using makeTranscriptDbFromUCSC() >>>>>> function*.* >>>>>> >>>>>> >>>>>> working code: >>>>>> >>>>>> mouseGNM <- makeTranscriptDbFromBiomart (biomart = "ensembl", dataset= >>>>>> "mmusculus_gene_ensembl"); >>>>>> saveDb(mouseGNM, file="MouseGNM.sqlite"); >>>>>> library("GenomicFeatures"); >>>>>> MouseGNM<- loadDb("MouseGNM.sqlite"); >>>>>> GenegroupedTranscripts<- transcriptsBy(MouseGNM, by = "gene"); >>>>>> strand.info <-as.integer(runValue(strand(GenegroupedTranscripts))); >>>>>> >>>>>> runValue(strand(GenegroupedTranscripts)) CompressedIntegerList of >>>>>> >>>>>>> length >>>>>>> >>>>>>> 37315 [["ENSMUSG00000000001"]] 2 [["ENSMUSG00000000003"]] 2 >>>>>> [["ENSMUSG00000000028"]] 2 [["ENSMUSG00000000031"]] 2 >>>>>> [["ENSMUSG00000000037"]] 1 [["ENSMUSG00000000049"]] 1 >>>>>> [["ENSMUSG00000000056"]] 1 [["ENSMUSG00000000058"]] 1 >>>>>> [["ENSMUSG00000000078"]] 1 [["ENSMUSG00000000085"]] 1 ... <37305 more >>>>>> elements> >>>>>> >>>>>> strand.info[1:100] >>>>>> >>>>>>> >>>>>>> [1] 2 2 2 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 2 1 1 1 2 1 2 1 1 2 2 1 >>>>>> 1 2 1 >>>>>> 2 2 >>>>>> 1 2 [38] 2 1 1 1 1 1 1 2 1 1 2 2 1 1 1 2 2 1 1 1 2 1 2 1 2 2 1 1 1 >>>>>> 1 1 2 >>>>>> 1 >>>>>> 2 2 2 2 [75] 2 2 2 2 2 2 2 1 2 1 1 2 2 2 1 1 1 2 1 2 2 2 1 1 2 1 >>>>>> >>>>>> here 2 is the antisense strand and 1 the sense strand >>>>>> >>>>>> >>>>>> UCSC.mouseGNM <- makeTranscriptDbFromUCSC(genome = "mm9", tablename = >>>>>> "knownGene"); >>>>>> saveDb(UCSC.mouseGNM, file="UCSCMouseGNM.sqlite"); >>>>>> UCSCMouseGNM<- loadDb("UCSCMouseGNM.sqlite"); >>>>>> UCSCGenegroupedTranscripts<- transcriptsBy(UCSCMouseGNM, by = "gene"); >>>>>> strand.info2<- >>>>>> as.integer(runValue(strand(UCSCGenegroupedTranscripts))); >>>>>> >>>>>> runValue(strand(UCSCGenegroupedTranscripts)) >>>>>> >>>>>>> >>>>>>> CompressedIntegerList of length 21761 >>>>>> [["100009600"]] 2 >>>>>> [["100009609"]] 2 >>>>>> [["100009614"]] 1 >>>>>> [["100012"]] 2 >>>>>> [["100017"]] 2 >>>>>> [["100019"]] 1 >>>>>> [["100033459"]] 1 >>>>>> [["100034251"]] 1 >>>>>> [["100034361"]] 2 >>>>>> [["100034684"]] 2 >>>>>> ... >>>>>> <21751 more elements> >>>>>> >>>>>> *ERROR:* >>>>>> >>>>>> strand.info2<- as.integer(runValue(strand( >>>>>> >>>>>>> UCSCGenegroupedTranscripts))); >>>>>>> >>>>>>> Error in as.vector(x, mode = "integer") : coercing an AtomicList >>>>>> object >>>>>> to >>>>>> an atomic vector is supported only for objects with top-level >>>>>> elements of >>>>>> length <= 1 >>>>>> >>>>>> I am not able to understand this error message, could anyone let me >>>>>> know >>>>>> what is going wrong in the code. >>>>>> Here is the session information. >>>>>> >>>>>> sessionInfo() R version 2.15.2 (2012-10-26) Platform: >>>>>> >>>>>>> x86_64-pc-linux-gnu >>>>>>> >>>>>>> (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] >>>>>> LC_TIME=en_US.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_US.UTF-8 >>>>>> LC_MESSAGES=en_AU.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] GenomicFeatures_1.10.1 >>>>>> AnnotationDbi_1.20.3 >>>>>> Biobase_2.18.0 [4] GenomicRanges_1.10.5 IRanges_1.16.4 >>>>>> BiocGenerics_0.4.0 >>>>>> loaded via a namespace (and not attached): [1] biomaRt_2.14.0 >>>>>> Biostrings_2.26.2 bitops_1.0-5 BSgenome_1.26.1 [5] DBI_0.2-5 >>>>>> parallel_2.15.2 RCurl_1.95-3 Rsamtools_1.10.2 [9] RSQLite_0.11.2 >>>>>> rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 [13] XML_3.95-0.1 >>>>>> zlibbioc_1.4.0 >>>>>> >>>>>> >>>>>> Thank you in advance. >>>>>> Regards, >>>>>> >>>>>> Veerendra. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> -- >>>> GP.Veerendra >>>> PhD Student (Bioinformatics) >>>> Stazione Zoologica Anton Dohrn >>>> Naples, Italy >>>> M:+393663915221 >>>> >>>> >>> >>> >>> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- Veerendra Gadekar PhD Student (Bioinformatics) Animal Physiology and Evolution Stazione Zoologica Anton Dohrn Villa Comunale, 80121 Naples - Italy M:+393663915221 [[alternative HTML version deleted]]