countOverlaps() only count positive strand (from GenomicRanges example)
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Song Li ▴ 60
@song-li-4383
Last seen 9.7 years ago
Hi All, I was following the example in the "GenomicRanges Use Cases", section 3, "Simple RNA-seq Analysis", by "copy-paste" command from the document from page 7 to page 8: What I found out is that countOverlap() only count reads aligned to positive strand. There are 28 reads map to region GRList[6645], 13 on positive strand, 15 on negative strand. The "count[6645]" is 13. Is there a way to count both strand? Thanks, Song Li Here are all the code: #-----> Start with code from the package description<-------# > library(Rsamtools) > testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") > aligns <- readBamGappedAlignments(testFile) > library(GenomicFeatures) > txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") > exonRanges <- exonsBy(txdb, "tx") > length(exonRanges) > levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), + sep = ""), "chrM") > counts <- countOverlaps(exonRanges, aligns) #-----> find alignments that map to GRList$6645<-------# > aligns[705:732] GappedAlignments of length 28 rname strand cigar qwidth start end width ngap [1] chrXIII + 36M 36 804443 804478 36 0 [2] chrXIII + 36M 36 804466 804501 36 0 [3] chrXIII - 36M 36 804473 804508 36 0 [4] chrXIII + 36M 36 804476 804511 36 0 [5] chrXIII - 36M 36 804493 804528 36 0 [6] chrXIII + 36M 36 804516 804551 36 0 [7] chrXIII + 36M 36 804562 804597 36 0 [8] chrXIII + 36M 36 804562 804597 36 0 [9] chrXIII - 36M 36 804574 804609 36 0 ... ... ... ... ... ... ... ... ... [20] chrXIII + 36M 36 804764 804799 36 0 [21] chrXIII - 36M 36 804798 804833 36 0 [22] chrXIII + 36M 36 804799 804834 36 0 [23] chrXIII + 36M 36 804799 804834 36 0 [24] chrXIII - 36M 36 804816 804851 36 0 [25] chrXIII - 36M 36 804947 804982 36 0 [26] chrXIII - 36M 36 804953 804988 36 0 [27] chrXIII - 36M 36 804955 804990 36 0 [28] chrXIII - 36M 36 804974 805009 36 0 > exonRanges[6646] GRangesList of length 1 $6646 GRanges with 1 range and 3 elementMetadata values seqnames ranges strand | exon_id exon_name exon_rank <rle> <iranges> <rle> | <integer> <character> <integer> [1] chrXIII [804455, 805090] + | 7011 NA 1 seqlengths chrIV chrXV chrVII chrXII chrXVI ... chrVI chrI chrM 2micron 1531919 1091289 1090947 1078175 948062 ... 270148 230208 85779 6318 > counts[6646] [1] 13 > table(strand(aligns[705:732])) + - 13 15 > sessionInfo() R version 2.12.0 (2010-10-15) 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=C 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] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.2.1 Biostrings_2.18.0 GenomicFeatures_1.2.3 [4] GenomicRanges_1.2.1 IRanges_1.8.2 loaded via a namespace (and not attached): [1] Biobase_2.10.0 biomaRt_2.6.0 BSgenome_1.18.1 DBI_0.2-5 [5] RCurl_1.4-3 RSQLite_0.9-3 rtracklayer_1.10.5 tools_2.12.0 [9] XML_3.2-0 Song Li -- Postdoctoral Associate Institute for Genome Sciences and Policy Duke University
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On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at="" gmail.com=""> wrote: > Hi All, > > I was following the example in the "GenomicRanges Use Cases", section > 3, "Simple RNA-seq Analysis", by "copy-paste" command from the > document from page 7 to page 8: > > What I found out is that countOverlap() only count reads aligned to > positive strand. ?There are 28 reads map to region GRList[6645], 13 on > positive strand, 15 on negative strand. ?The "count[6645]" is 13. > > Is there a way to count both strand? If you want to disregard strand of exon range, set it to "*". This does not appear to be a one-liner. > > Thanks, > Song Li > > Here are all the code: > #-----> Start with code from the package description<-------# >> library(Rsamtools) >> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") >> aligns <- readBamGappedAlignments(testFile) >> library(GenomicFeatures) >> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") >> exonRanges <- exonsBy(txdb, "tx") >> length(exonRanges) >> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), > + ? ? sep = ""), "chrM") >> counts <- countOverlaps(exonRanges, aligns) > > #-----> find alignments that map to GRList$6645<-------# >> aligns[705:732] > GappedAlignments of length 28 > ? ? ? rname strand cigar qwidth ?start ? ?end width ngap > [1] ?chrXIII ? ? ?+ ? 36M ? ? 36 804443 804478 ? ?36 ? ?0 > [2] ?chrXIII ? ? ?+ ? 36M ? ? 36 804466 804501 ? ?36 ? ?0 > [3] ?chrXIII ? ? ?- ? 36M ? ? 36 804473 804508 ? ?36 ? ?0 > [4] ?chrXIII ? ? ?+ ? 36M ? ? 36 804476 804511 ? ?36 ? ?0 > [5] ?chrXIII ? ? ?- ? 36M ? ? 36 804493 804528 ? ?36 ? ?0 > [6] ?chrXIII ? ? ?+ ? 36M ? ? 36 804516 804551 ? ?36 ? ?0 > [7] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 > [8] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 > [9] ?chrXIII ? ? ?- ? 36M ? ? 36 804574 804609 ? ?36 ? ?0 > ... ? ? ?... ? ?... ? ... ? ?... ? ?... ? ?... ? ... ?... > [20] chrXIII ? ? ?+ ? 36M ? ? 36 804764 804799 ? ?36 ? ?0 > [21] chrXIII ? ? ?- ? 36M ? ? 36 804798 804833 ? ?36 ? ?0 > [22] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 > [23] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 > [24] chrXIII ? ? ?- ? 36M ? ? 36 804816 804851 ? ?36 ? ?0 > [25] chrXIII ? ? ?- ? 36M ? ? 36 804947 804982 ? ?36 ? ?0 > [26] chrXIII ? ? ?- ? 36M ? ? 36 804953 804988 ? ?36 ? ?0 > [27] chrXIII ? ? ?- ? 36M ? ? 36 804955 804990 ? ?36 ? ?0 > [28] chrXIII ? ? ?- ? 36M ? ? 36 804974 805009 ? ?36 ? ?0 >> exonRanges[6646] > GRangesList of length 1 > $6646 > GRanges with 1 range and 3 elementMetadata values > ? ?seqnames ? ? ? ? ? ranges strand | ? exon_id ? exon_name exon_rank > ? ? ? <rle> ? ? ? ?<iranges> ?<rle> | <integer> <character> <integer> > [1] ?chrXIII [804455, 805090] ? ? ?+ | ? ? ?7011 ? ? ? ? ?NA ? ? ? ? 1 > > > seqlengths > ? chrIV ? chrXV ?chrVII ?chrXII ?chrXVI ... ? chrVI ? ?chrI ? ?chrM 2micron > ?1531919 1091289 1090947 1078175 ?948062 ... ?270148 ?230208 ? 85779 ? ?6318 >> counts[6646] > [1] 13 >> table(strand(aligns[705:732])) > > ?+ ?- > 13 15 > > >> sessionInfo() > R version 2.12.0 (2010-10-15) > 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=C ? ? ? ? ? ? ?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] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] Rsamtools_1.2.1 ? ? ? Biostrings_2.18.0 ? ? GenomicFeatures_1.2.3 > [4] GenomicRanges_1.2.1 ? IRanges_1.8.2 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 ? ? biomaRt_2.6.0 ? ? ?BSgenome_1.18.1 ? ?DBI_0.2-5 > [5] RCurl_1.4-3 ? ? ? ?RSQLite_0.9-3 ? ? ?rtracklayer_1.10.5 tools_2.12.0 > [9] XML_3.2-0 > > Song Li > -- > Postdoctoral Associate > Institute for Genome Sciences and Policy > Duke University > > _______________________________________________ > 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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On 12/13/2010 09:30 AM, Vincent Carey wrote: > On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at="" gmail.com=""> wrote: >> Hi All, >> >> I was following the example in the "GenomicRanges Use Cases", section >> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the >> document from page 7 to page 8: >> >> What I found out is that countOverlap() only count reads aligned to >> positive strand. There are 28 reads map to region GRList[6645], 13 on >> positive strand, 15 on negative strand. The "count[6645]" is 13. >> >> Is there a way to count both strand? > > If you want to disregard strand of exon range, set it to "*". This > does not appear to be a one-liner. it's tricky to set strand() on a GappedAlignment (because the CIGAR has to be adjusted appropriately) but the I believe that the converse strand(exonRanges) <- "*" accomplishes the same goal -- reads are counted without regard to strand of alignment. Martin > >> >> Thanks, >> Song Li >> >> Here are all the code: >> #-----> Start with code from the package description<-------# >>> library(Rsamtools) >>> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") >>> aligns <- readBamGappedAlignments(testFile) >>> library(GenomicFeatures) >>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") >>> exonRanges <- exonsBy(txdb, "tx") >>> length(exonRanges) >>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), >> + sep = ""), "chrM") >>> counts <- countOverlaps(exonRanges, aligns) >> >> #-----> find alignments that map to GRList$6645<-------# >>> aligns[705:732] >> GappedAlignments of length 28 >> rname strand cigar qwidth start end width ngap >> [1] chrXIII + 36M 36 804443 804478 36 0 >> [2] chrXIII + 36M 36 804466 804501 36 0 >> [3] chrXIII - 36M 36 804473 804508 36 0 >> [4] chrXIII + 36M 36 804476 804511 36 0 >> [5] chrXIII - 36M 36 804493 804528 36 0 >> [6] chrXIII + 36M 36 804516 804551 36 0 >> [7] chrXIII + 36M 36 804562 804597 36 0 >> [8] chrXIII + 36M 36 804562 804597 36 0 >> [9] chrXIII - 36M 36 804574 804609 36 0 >> ... ... ... ... ... ... ... ... ... >> [20] chrXIII + 36M 36 804764 804799 36 0 >> [21] chrXIII - 36M 36 804798 804833 36 0 >> [22] chrXIII + 36M 36 804799 804834 36 0 >> [23] chrXIII + 36M 36 804799 804834 36 0 >> [24] chrXIII - 36M 36 804816 804851 36 0 >> [25] chrXIII - 36M 36 804947 804982 36 0 >> [26] chrXIII - 36M 36 804953 804988 36 0 >> [27] chrXIII - 36M 36 804955 804990 36 0 >> [28] chrXIII - 36M 36 804974 805009 36 0 >>> exonRanges[6646] >> GRangesList of length 1 >> $6646 >> GRanges with 1 range and 3 elementMetadata values >> seqnames ranges strand | exon_id exon_name exon_rank >> <rle> <iranges> <rle> | <integer> <character> <integer> >> [1] chrXIII [804455, 805090] + | 7011 NA 1 >> >> >> seqlengths >> chrIV chrXV chrVII chrXII chrXVI ... chrVI chrI chrM 2micron >> 1531919 1091289 1090947 1078175 948062 ... 270148 230208 85779 6318 >>> counts[6646] >> [1] 13 >>> table(strand(aligns[705:732])) >> >> + - >> 13 15 >> >> >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> 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=C 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] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] Rsamtools_1.2.1 Biostrings_2.18.0 GenomicFeatures_1.2.3 >> [4] GenomicRanges_1.2.1 IRanges_1.8.2 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.10.0 biomaRt_2.6.0 BSgenome_1.18.1 DBI_0.2-5 >> [5] RCurl_1.4-3 RSQLite_0.9-3 rtracklayer_1.10.5 tools_2.12.0 >> [9] XML_3.2-0 >> >> Song Li >> -- >> Postdoctoral Associate >> Institute for Genome Sciences and Policy >> Duke University >> >> _______________________________________________ >> 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi Martin and Vincent, Thank you for your replies, here is my code: > strand(exonRanges)<-"*" Error in `strand<-`(`*tmp*`, value = "*") : replacement 'value' is not an AtomicList with the same elementLengths as 'x' > levels(strand(aligns))<-c('*','*','*') Error in function (classes, fdef, mtable) : unable to find an inherited method for function "strand<-", for signature "GappedAlignments" It does not seem to be that straightforward. I have been searching for ways to make modification to the GappedAlignments and GRangesList objects. Song On Mon, Dec 13, 2010 at 12:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 12/13/2010 09:30 AM, Vincent Carey wrote: >> On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at="" gmail.com=""> wrote: >>> Hi All, >>> >>> I was following the example in the "GenomicRanges Use Cases", section >>> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the >>> document from page 7 to page 8: >>> >>> What I found out is that countOverlap() only count reads aligned to >>> positive strand. ?There are 28 reads map to region GRList[6645], 13 on >>> positive strand, 15 on negative strand. ?The "count[6645]" is 13. >>> >>> Is there a way to count both strand? >> >> If you want to disregard strand of exon range, set it to "*". ?This >> does not appear to be a one-liner. > > it's tricky to set strand() on a GappedAlignment (because the CIGAR has > to be adjusted appropriately) but the I believe that the converse > > ?strand(exonRanges) <- "*" > > accomplishes the same goal -- reads are counted without regard to strand > of alignment. > > Martin > >> >>> >>> Thanks, >>> Song Li >>> >>> Here are all the code: >>> #-----> Start with code from the package description<-------# >>>> library(Rsamtools) >>>> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") >>>> aligns <- readBamGappedAlignments(testFile) >>>> library(GenomicFeatures) >>>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") >>>> exonRanges <- exonsBy(txdb, "tx") >>>> length(exonRanges) >>>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), >>> + ? ? sep = ""), "chrM") >>>> counts <- countOverlaps(exonRanges, aligns) >>> >>> #-----> find alignments that map to GRList$6645<-------# >>>> aligns[705:732] >>> GappedAlignments of length 28 >>> ? ? ? rname strand cigar qwidth ?start ? ?end width ngap >>> [1] ?chrXIII ? ? ?+ ? 36M ? ? 36 804443 804478 ? ?36 ? ?0 >>> [2] ?chrXIII ? ? ?+ ? 36M ? ? 36 804466 804501 ? ?36 ? ?0 >>> [3] ?chrXIII ? ? ?- ? 36M ? ? 36 804473 804508 ? ?36 ? ?0 >>> [4] ?chrXIII ? ? ?+ ? 36M ? ? 36 804476 804511 ? ?36 ? ?0 >>> [5] ?chrXIII ? ? ?- ? 36M ? ? 36 804493 804528 ? ?36 ? ?0 >>> [6] ?chrXIII ? ? ?+ ? 36M ? ? 36 804516 804551 ? ?36 ? ?0 >>> [7] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 >>> [8] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 >>> [9] ?chrXIII ? ? ?- ? 36M ? ? 36 804574 804609 ? ?36 ? ?0 >>> ... ? ? ?... ? ?... ? ... ? ?... ? ?... ? ?... ? ... ?... >>> [20] chrXIII ? ? ?+ ? 36M ? ? 36 804764 804799 ? ?36 ? ?0 >>> [21] chrXIII ? ? ?- ? 36M ? ? 36 804798 804833 ? ?36 ? ?0 >>> [22] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 >>> [23] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 >>> [24] chrXIII ? ? ?- ? 36M ? ? 36 804816 804851 ? ?36 ? ?0 >>> [25] chrXIII ? ? ?- ? 36M ? ? 36 804947 804982 ? ?36 ? ?0 >>> [26] chrXIII ? ? ?- ? 36M ? ? 36 804953 804988 ? ?36 ? ?0 >>> [27] chrXIII ? ? ?- ? 36M ? ? 36 804955 804990 ? ?36 ? ?0 >>> [28] chrXIII ? ? ?- ? 36M ? ? 36 804974 805009 ? ?36 ? ?0 >>>> exonRanges[6646] >>> GRangesList of length 1 >>> $6646 >>> GRanges with 1 range and 3 elementMetadata values >>> ? ?seqnames ? ? ? ? ? ranges strand | ? exon_id ? exon_name exon_rank >>> ? ? ? <rle> ? ? ? ?<iranges> ?<rle> | <integer> <character> <integer> >>> [1] ?chrXIII [804455, 805090] ? ? ?+ | ? ? ?7011 ? ? ? ? ?NA ? ? ? ? 1 >>> >>> >>> seqlengths >>> ? chrIV ? chrXV ?chrVII ?chrXII ?chrXVI ... ? chrVI ? ?chrI ? ?chrM 2micron >>> ?1531919 1091289 1090947 1078175 ?948062 ... ?270148 ?230208 ? 85779 ? ?6318 >>>> counts[6646] >>> [1] 13 >>>> table(strand(aligns[705:732])) >>> >>> ?+ ?- >>> 13 15 >>> >>> >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> 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=C ? ? ? ? ? ? ?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] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] Rsamtools_1.2.1 ? ? ? Biostrings_2.18.0 ? ? GenomicFeatures_1.2.3 >>> [4] GenomicRanges_1.2.1 ? IRanges_1.8.2 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.10.0 ? ? biomaRt_2.6.0 ? ? ?BSgenome_1.18.1 ? ?DBI_0.2-5 >>> [5] RCurl_1.4-3 ? ? ? ?RSQLite_0.9-3 ? ? ?rtracklayer_1.10.5 tools_2.12.0 >>> [9] XML_3.2-0 >>> >>> Song Li >>> -- >>> Postdoctoral Associate >>> Institute for Genome Sciences and Policy >>> Duke University >>> >>> _______________________________________________ >>> 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 > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > -- Postdoctoral Associate Institute for Genome Sciences and Policy Duke University
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On 12/13/2010 10:09 AM, Song Li wrote: > Hi Martin and Vincent, > > Thank you for your replies, here is my code: > >> strand(exonRanges)<-"*" > Error in `strand<-`(`*tmp*`, value = "*") : > replacement 'value' is not an AtomicList with the same elementLengths as 'x' create a list of character vectors, each of the appropriate length value <- lapply(elementLengths(exonRanges), rep, x="*") convert this list to a class derived from 'AtomicList', and do the replacement strand(exonRanges) <- CharacterList(value) Sometimes it's easier / faster to work with exons(txdb, column="tx_id") or similar. Martin > >> levels(strand(aligns))<-c('*','*','*') > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "strand<-", for > signature "GappedAlignments" > > It does not seem to be that straightforward. > > I have been searching for ways to make modification to the > GappedAlignments and GRangesList objects. > > Song > > On Mon, Dec 13, 2010 at 12:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> On 12/13/2010 09:30 AM, Vincent Carey wrote: >>> On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at="" gmail.com=""> wrote: >>>> Hi All, >>>> >>>> I was following the example in the "GenomicRanges Use Cases", section >>>> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the >>>> document from page 7 to page 8: >>>> >>>> What I found out is that countOverlap() only count reads aligned to >>>> positive strand. There are 28 reads map to region GRList[6645], 13 on >>>> positive strand, 15 on negative strand. The "count[6645]" is 13. >>>> >>>> Is there a way to count both strand? >>> >>> If you want to disregard strand of exon range, set it to "*". This >>> does not appear to be a one-liner. >> >> it's tricky to set strand() on a GappedAlignment (because the CIGAR has >> to be adjusted appropriately) but the I believe that the converse >> >> strand(exonRanges) <- "*" >> >> accomplishes the same goal -- reads are counted without regard to strand >> of alignment. >> >> Martin >> >>> >>>> >>>> Thanks, >>>> Song Li >>>> >>>> Here are all the code: >>>> #-----> Start with code from the package description<-------# >>>>> library(Rsamtools) >>>>> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") >>>>> aligns <- readBamGappedAlignments(testFile) >>>>> library(GenomicFeatures) >>>>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") >>>>> exonRanges <- exonsBy(txdb, "tx") >>>>> length(exonRanges) >>>>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), >>>> + sep = ""), "chrM") >>>>> counts <- countOverlaps(exonRanges, aligns) >>>> >>>> #-----> find alignments that map to GRList$6645<-------# >>>>> aligns[705:732] >>>> GappedAlignments of length 28 >>>> rname strand cigar qwidth start end width ngap >>>> [1] chrXIII + 36M 36 804443 804478 36 0 >>>> [2] chrXIII + 36M 36 804466 804501 36 0 >>>> [3] chrXIII - 36M 36 804473 804508 36 0 >>>> [4] chrXIII + 36M 36 804476 804511 36 0 >>>> [5] chrXIII - 36M 36 804493 804528 36 0 >>>> [6] chrXIII + 36M 36 804516 804551 36 0 >>>> [7] chrXIII + 36M 36 804562 804597 36 0 >>>> [8] chrXIII + 36M 36 804562 804597 36 0 >>>> [9] chrXIII - 36M 36 804574 804609 36 0 >>>> ... ... ... ... ... ... ... ... ... >>>> [20] chrXIII + 36M 36 804764 804799 36 0 >>>> [21] chrXIII - 36M 36 804798 804833 36 0 >>>> [22] chrXIII + 36M 36 804799 804834 36 0 >>>> [23] chrXIII + 36M 36 804799 804834 36 0 >>>> [24] chrXIII - 36M 36 804816 804851 36 0 >>>> [25] chrXIII - 36M 36 804947 804982 36 0 >>>> [26] chrXIII - 36M 36 804953 804988 36 0 >>>> [27] chrXIII - 36M 36 804955 804990 36 0 >>>> [28] chrXIII - 36M 36 804974 805009 36 0 >>>>> exonRanges[6646] >>>> GRangesList of length 1 >>>> $6646 >>>> GRanges with 1 range and 3 elementMetadata values >>>> seqnames ranges strand | exon_id exon_name exon_rank >>>> <rle> <iranges> <rle> | <integer> <character> <integer> >>>> [1] chrXIII [804455, 805090] + | 7011 NA 1 >>>> >>>> >>>> seqlengths >>>> chrIV chrXV chrVII chrXII chrXVI ... chrVI chrI chrM 2micron >>>> 1531919 1091289 1090947 1078175 948062 ... 270148 230208 85779 6318 >>>>> counts[6646] >>>> [1] 13 >>>>> table(strand(aligns[705:732])) >>>> >>>> + - >>>> 13 15 >>>> >>>> >>>>> sessionInfo() >>>> R version 2.12.0 (2010-10-15) >>>> 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=C 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] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] Rsamtools_1.2.1 Biostrings_2.18.0 GenomicFeatures_1.2.3 >>>> [4] GenomicRanges_1.2.1 IRanges_1.8.2 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.10.0 biomaRt_2.6.0 BSgenome_1.18.1 DBI_0.2-5 >>>> [5] RCurl_1.4-3 RSQLite_0.9-3 rtracklayer_1.10.5 tools_2.12.0 >>>> [9] XML_3.2-0 >>>> >>>> Song Li >>>> -- >>>> Postdoctoral Associate >>>> Institute for Genome Sciences and Policy >>>> Duke University >>>> >>>> _______________________________________________ >>>> 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 >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi Martin and Vincent, Thank you for the replies and both methods work, Cheers, Song On Mon, Dec 13, 2010 at 2:19 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 12/13/2010 10:09 AM, Song Li wrote: >> Hi Martin and Vincent, >> >> Thank you for your replies, here is my code: >> >>> strand(exonRanges)<-"*" >> Error in `strand<-`(`*tmp*`, value = "*") : >> ? replacement 'value' is not an AtomicList with the same elementLengths as 'x' > > create a list of character vectors, each of the appropriate length > > ?value <- lapply(elementLengths(exonRanges), rep, x="*") > > convert this list to a class derived from 'AtomicList', and do the > replacement > > ?strand(exonRanges) <- CharacterList(value) > > Sometimes it's easier / faster to work with exons(txdb, column="tx_id") > or similar. > > Martin > > >> >>> levels(strand(aligns))<-c('*','*','*') >> Error in function (classes, fdef, mtable) ?: >> ? unable to find an inherited method for function "strand<-", for >> signature "GappedAlignments" >> >> It does not seem to be that straightforward. >> >> I have been searching for ways to make modification to the >> GappedAlignments and GRangesList ?objects. >> >> Song >> >> On Mon, Dec 13, 2010 at 12:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >>> On 12/13/2010 09:30 AM, Vincent Carey wrote: >>>> On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at="" gmail.com=""> wrote: >>>>> Hi All, >>>>> >>>>> I was following the example in the "GenomicRanges Use Cases", section >>>>> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the >>>>> document from page 7 to page 8: >>>>> >>>>> What I found out is that countOverlap() only count reads aligned to >>>>> positive strand. ?There are 28 reads map to region GRList[6645], 13 on >>>>> positive strand, 15 on negative strand. ?The "count[6645]" is 13. >>>>> >>>>> Is there a way to count both strand? >>>> >>>> If you want to disregard strand of exon range, set it to "*". ?This >>>> does not appear to be a one-liner. >>> >>> it's tricky to set strand() on a GappedAlignment (because the CIGAR has >>> to be adjusted appropriately) but the I believe that the converse >>> >>> ?strand(exonRanges) <- "*" >>> >>> accomplishes the same goal -- reads are counted without regard to strand >>> of alignment. >>> >>> Martin >>> >>>> >>>>> >>>>> Thanks, >>>>> Song Li >>>>> >>>>> Here are all the code: >>>>> #-----> Start with code from the package description<-------# >>>>>> library(Rsamtools) >>>>>> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") >>>>>> aligns <- readBamGappedAlignments(testFile) >>>>>> library(GenomicFeatures) >>>>>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") >>>>>> exonRanges <- exonsBy(txdb, "tx") >>>>>> length(exonRanges) >>>>>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), >>>>> + ? ? sep = ""), "chrM") >>>>>> counts <- countOverlaps(exonRanges, aligns) >>>>> >>>>> #-----> find alignments that map to GRList$6645<-------# >>>>>> aligns[705:732] >>>>> GappedAlignments of length 28 >>>>> ? ? ? rname strand cigar qwidth ?start ? ?end width ngap >>>>> [1] ?chrXIII ? ? ?+ ? 36M ? ? 36 804443 804478 ? ?36 ? ?0 >>>>> [2] ?chrXIII ? ? ?+ ? 36M ? ? 36 804466 804501 ? ?36 ? ?0 >>>>> [3] ?chrXIII ? ? ?- ? 36M ? ? 36 804473 804508 ? ?36 ? ?0 >>>>> [4] ?chrXIII ? ? ?+ ? 36M ? ? 36 804476 804511 ? ?36 ? ?0 >>>>> [5] ?chrXIII ? ? ?- ? 36M ? ? 36 804493 804528 ? ?36 ? ?0 >>>>> [6] ?chrXIII ? ? ?+ ? 36M ? ? 36 804516 804551 ? ?36 ? ?0 >>>>> [7] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 >>>>> [8] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 >>>>> [9] ?chrXIII ? ? ?- ? 36M ? ? 36 804574 804609 ? ?36 ? ?0 >>>>> ... ? ? ?... ? ?... ? ... ? ?... ? ?... ? ?... ? ... ?... >>>>> [20] chrXIII ? ? ?+ ? 36M ? ? 36 804764 804799 ? ?36 ? ?0 >>>>> [21] chrXIII ? ? ?- ? 36M ? ? 36 804798 804833 ? ?36 ? ?0 >>>>> [22] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 >>>>> [23] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 >>>>> [24] chrXIII ? ? ?- ? 36M ? ? 36 804816 804851 ? ?36 ? ?0 >>>>> [25] chrXIII ? ? ?- ? 36M ? ? 36 804947 804982 ? ?36 ? ?0 >>>>> [26] chrXIII ? ? ?- ? 36M ? ? 36 804953 804988 ? ?36 ? ?0 >>>>> [27] chrXIII ? ? ?- ? 36M ? ? 36 804955 804990 ? ?36 ? ?0 >>>>> [28] chrXIII ? ? ?- ? 36M ? ? 36 804974 805009 ? ?36 ? ?0 >>>>>> exonRanges[6646] >>>>> GRangesList of length 1 >>>>> $6646 >>>>> GRanges with 1 range and 3 elementMetadata values >>>>> ? ?seqnames ? ? ? ? ? ranges strand | ? exon_id ? exon_name exon_rank >>>>> ? ? ? <rle> ? ? ? ?<iranges> ?<rle> | <integer> <character> <integer> >>>>> [1] ?chrXIII [804455, 805090] ? ? ?+ | ? ? ?7011 ? ? ? ? ?NA ? ? ? ? 1 >>>>> >>>>> >>>>> seqlengths >>>>> ? chrIV ? chrXV ?chrVII ?chrXII ?chrXVI ... ? chrVI ? ?chrI ? ?chrM 2micron >>>>> ?1531919 1091289 1090947 1078175 ?948062 ... ?270148 ?230208 ? 85779 ? ?6318 >>>>>> counts[6646] >>>>> [1] 13 >>>>>> table(strand(aligns[705:732])) >>>>> >>>>> ?+ ?- >>>>> 13 15 >>>>> >>>>> >>>>>> sessionInfo() >>>>> R version 2.12.0 (2010-10-15) >>>>> 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=C ? ? ? ? ? ? ?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] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>> >>>>> other attached packages: >>>>> [1] Rsamtools_1.2.1 ? ? ? Biostrings_2.18.0 ? ? GenomicFeatures_1.2.3 >>>>> [4] GenomicRanges_1.2.1 ? IRanges_1.8.2 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] Biobase_2.10.0 ? ? biomaRt_2.6.0 ? ? ?BSgenome_1.18.1 ? ?DBI_0.2-5 >>>>> [5] RCurl_1.4-3 ? ? ? ?RSQLite_0.9-3 ? ? ?rtracklayer_1.10.5 tools_2.12.0 >>>>> [9] XML_3.2-0 >>>>> >>>>> Song Li >>>>> -- >>>>> Postdoctoral Associate >>>>> Institute for Genome Sciences and Policy >>>>> Duke University >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >>> >> >> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > -- Postdoctoral Associate Institute for Genome Sciences and Policy Duke University
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On Mon, Dec 13, 2010 at 11:19 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 12/13/2010 10:09 AM, Song Li wrote: > > Hi Martin and Vincent, > > > > Thank you for your replies, here is my code: > > > >> strand(exonRanges)<-"*" > > Error in `strand<-`(`*tmp*`, value = "*") : > > replacement 'value' is not an AtomicList with the same elementLengths > as 'x' > > create a list of character vectors, each of the appropriate length > > value <- lapply(elementLengths(exonRanges), rep, x="*") > > Just for the record, seqapply is useful here, as it automatically does the casting to CharacterList: value <- seqapply(elementLengths(exonRanges), rep, x="*") Even though rep is a primitive, it's generally faster but messier to do this with rep/seq_len, i.e., el <- elementLengths(exonRanges) strand(exonRanges) <- seqsplit(rep("*", sum(el)), rep(seq_len(length(exonRanges)), el)) Note that 'seqsplit' also does the automatic coercion. I'll soon check in an optimization to create a CompressedCharacterList without actually splitting anything. This is more efficient in time and space. convert this list to a class derived from 'AtomicList', and do the > replacement > > strand(exonRanges) <- CharacterList(value) > > Sometimes it's easier / faster to work with exons(txdb, column="tx_id") > or similar. > > Martin > > > > > >> levels(strand(aligns))<-c('*','*','*') > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function "strand<-", for > > signature "GappedAlignments" > > > > It does not seem to be that straightforward. > > > > I have been searching for ways to make modification to the > > GappedAlignments and GRangesList objects. > > > > Song > > > > On Mon, Dec 13, 2010 at 12:39 PM, Martin Morgan <mtmorgan@fhcrc.org> > wrote: > >> On 12/13/2010 09:30 AM, Vincent Carey wrote: > >>> On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116@gmail.com> wrote: > >>>> Hi All, > >>>> > >>>> I was following the example in the "GenomicRanges Use Cases", section > >>>> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the > >>>> document from page 7 to page 8: > >>>> > >>>> What I found out is that countOverlap() only count reads aligned to > >>>> positive strand. There are 28 reads map to region GRList[6645], 13 on > >>>> positive strand, 15 on negative strand. The "count[6645]" is 13. > >>>> > >>>> Is there a way to count both strand? > >>> > >>> If you want to disregard strand of exon range, set it to "*". This > >>> does not appear to be a one-liner. > >> > >> it's tricky to set strand() on a GappedAlignment (because the CIGAR has > >> to be adjusted appropriately) but the I believe that the converse > >> > >> strand(exonRanges) <- "*" > >> > >> accomplishes the same goal -- reads are counted without regard to strand > >> of alignment. > >> > >> Martin > >> > >>> > >>>> > >>>> Thanks, > >>>> Song Li > >>>> > >>>> Here are all the code: > >>>> #-----> Start with code from the package description<-------# > >>>>> library(Rsamtools) > >>>>> testFile <- system.file("bam", "isowt5_13e.bam", package = > "leeBamViews") > >>>>> aligns <- readBamGappedAlignments(testFile) > >>>>> library(GenomicFeatures) > >>>>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = > "sgdGene") > >>>>> exonRanges <- exonsBy(txdb, "tx") > >>>>> length(exonRanges) > >>>>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), > >>>> + sep = ""), "chrM") > >>>>> counts <- countOverlaps(exonRanges, aligns) > >>>> > >>>> #-----> find alignments that map to GRList$6645<-------# > >>>>> aligns[705:732] > >>>> GappedAlignments of length 28 > >>>> rname strand cigar qwidth start end width ngap > >>>> [1] chrXIII + 36M 36 804443 804478 36 0 > >>>> [2] chrXIII + 36M 36 804466 804501 36 0 > >>>> [3] chrXIII - 36M 36 804473 804508 36 0 > >>>> [4] chrXIII + 36M 36 804476 804511 36 0 > >>>> [5] chrXIII - 36M 36 804493 804528 36 0 > >>>> [6] chrXIII + 36M 36 804516 804551 36 0 > >>>> [7] chrXIII + 36M 36 804562 804597 36 0 > >>>> [8] chrXIII + 36M 36 804562 804597 36 0 > >>>> [9] chrXIII - 36M 36 804574 804609 36 0 > >>>> ... ... ... ... ... ... ... ... ... > >>>> [20] chrXIII + 36M 36 804764 804799 36 0 > >>>> [21] chrXIII - 36M 36 804798 804833 36 0 > >>>> [22] chrXIII + 36M 36 804799 804834 36 0 > >>>> [23] chrXIII + 36M 36 804799 804834 36 0 > >>>> [24] chrXIII - 36M 36 804816 804851 36 0 > >>>> [25] chrXIII - 36M 36 804947 804982 36 0 > >>>> [26] chrXIII - 36M 36 804953 804988 36 0 > >>>> [27] chrXIII - 36M 36 804955 804990 36 0 > >>>> [28] chrXIII - 36M 36 804974 805009 36 0 > >>>>> exonRanges[6646] > >>>> GRangesList of length 1 > >>>> $6646 > >>>> GRanges with 1 range and 3 elementMetadata values > >>>> seqnames ranges strand | exon_id exon_name exon_rank > >>>> <rle> <iranges> <rle> | <integer> <character> <integer> > >>>> [1] chrXIII [804455, 805090] + | 7011 NA 1 > >>>> > >>>> > >>>> seqlengths > >>>> chrIV chrXV chrVII chrXII chrXVI ... chrVI chrI chrM > 2micron > >>>> 1531919 1091289 1090947 1078175 948062 ... 270148 230208 85779 > 6318 > >>>>> counts[6646] > >>>> [1] 13 > >>>>> table(strand(aligns[705:732])) > >>>> > >>>> + - > >>>> 13 15 > >>>> > >>>> > >>>>> sessionInfo() > >>>> R version 2.12.0 (2010-10-15) > >>>> 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=C 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] stats graphics grDevices utils datasets methods base > >>>> > >>>> other attached packages: > >>>> [1] Rsamtools_1.2.1 Biostrings_2.18.0 GenomicFeatures_1.2.3 > >>>> [4] GenomicRanges_1.2.1 IRanges_1.8.2 > >>>> > >>>> loaded via a namespace (and not attached): > >>>> [1] Biobase_2.10.0 biomaRt_2.6.0 BSgenome_1.18.1 DBI_0.2-5 > >>>> [5] RCurl_1.4-3 RSQLite_0.9-3 rtracklayer_1.10.5 > tools_2.12.0 > >>>> [9] XML_3.2-0 > >>>> > >>>> Song Li > >>>> -- > >>>> Postdoctoral Associate > >>>> Institute for Genome Sciences and Policy > >>>> Duke University > >>>> > >>>> _______________________________________________ > >>>> Bioconductor mailing list > >>>> Bioconductor@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@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > >> -- > >> Computational Biology > >> Fred Hutchinson Cancer Research Center > >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > >> > >> Location: M1-B861 > >> Telephone: 206 667-2793 > >> > > > > > > > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]
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For the nonce, the solution is to make the AtomicList with the desired content and reassign ser = strand(exonRanges) ss = endoapply(ser, function(x){x[] = "*"; x}) # overkill? slow... strand(exonRanges) = ss cc = countOverlaps(exonRanges, aligns) cc[6646] On Mon, Dec 13, 2010 at 1:09 PM, Song Li <songli116 at="" gmail.com=""> wrote: > Hi Martin and Vincent, > > Thank you for your replies, here is my code: > >> strand(exonRanges)<-"*" > Error in `strand<-`(`*tmp*`, value = "*") : > ?replacement 'value' is not an AtomicList with the same elementLengths as 'x' > >> levels(strand(aligns))<-c('*','*','*') > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "strand<-", for > signature "GappedAlignments" > > It does not seem to be that straightforward. > > I have been searching for ways to make modification to the > GappedAlignments and GRangesList ?objects. > > Song > > On Mon, Dec 13, 2010 at 12:39 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> On 12/13/2010 09:30 AM, Vincent Carey wrote: >>> On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at="" gmail.com=""> wrote: >>>> Hi All, >>>> >>>> I was following the example in the "GenomicRanges Use Cases", section >>>> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the >>>> document from page 7 to page 8: >>>> >>>> What I found out is that countOverlap() only count reads aligned to >>>> positive strand. ?There are 28 reads map to region GRList[6645], 13 on >>>> positive strand, 15 on negative strand. ?The "count[6645]" is 13. >>>> >>>> Is there a way to count both strand? >>> >>> If you want to disregard strand of exon range, set it to "*". ?This >>> does not appear to be a one-liner. >> >> it's tricky to set strand() on a GappedAlignment (because the CIGAR has >> to be adjusted appropriately) but the I believe that the converse >> >> ?strand(exonRanges) <- "*" >> >> accomplishes the same goal -- reads are counted without regard to strand >> of alignment. >> >> Martin >> >>> >>>> >>>> Thanks, >>>> Song Li >>>> >>>> Here are all the code: >>>> #-----> Start with code from the package description<-------# >>>>> library(Rsamtools) >>>>> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews") >>>>> aligns <- readBamGappedAlignments(testFile) >>>>> library(GenomicFeatures) >>>>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene") >>>>> exonRanges <- exonsBy(txdb, "tx") >>>>> length(exonRanges) >>>>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16), >>>> + ? ? sep = ""), "chrM") >>>>> counts <- countOverlaps(exonRanges, aligns) >>>> >>>> #-----> find alignments that map to GRList$6645<-------# >>>>> aligns[705:732] >>>> GappedAlignments of length 28 >>>> ? ? ? rname strand cigar qwidth ?start ? ?end width ngap >>>> [1] ?chrXIII ? ? ?+ ? 36M ? ? 36 804443 804478 ? ?36 ? ?0 >>>> [2] ?chrXIII ? ? ?+ ? 36M ? ? 36 804466 804501 ? ?36 ? ?0 >>>> [3] ?chrXIII ? ? ?- ? 36M ? ? 36 804473 804508 ? ?36 ? ?0 >>>> [4] ?chrXIII ? ? ?+ ? 36M ? ? 36 804476 804511 ? ?36 ? ?0 >>>> [5] ?chrXIII ? ? ?- ? 36M ? ? 36 804493 804528 ? ?36 ? ?0 >>>> [6] ?chrXIII ? ? ?+ ? 36M ? ? 36 804516 804551 ? ?36 ? ?0 >>>> [7] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 >>>> [8] ?chrXIII ? ? ?+ ? 36M ? ? 36 804562 804597 ? ?36 ? ?0 >>>> [9] ?chrXIII ? ? ?- ? 36M ? ? 36 804574 804609 ? ?36 ? ?0 >>>> ... ? ? ?... ? ?... ? ... ? ?... ? ?... ? ?... ? ... ?... >>>> [20] chrXIII ? ? ?+ ? 36M ? ? 36 804764 804799 ? ?36 ? ?0 >>>> [21] chrXIII ? ? ?- ? 36M ? ? 36 804798 804833 ? ?36 ? ?0 >>>> [22] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 >>>> [23] chrXIII ? ? ?+ ? 36M ? ? 36 804799 804834 ? ?36 ? ?0 >>>> [24] chrXIII ? ? ?- ? 36M ? ? 36 804816 804851 ? ?36 ? ?0 >>>> [25] chrXIII ? ? ?- ? 36M ? ? 36 804947 804982 ? ?36 ? ?0 >>>> [26] chrXIII ? ? ?- ? 36M ? ? 36 804953 804988 ? ?36 ? ?0 >>>> [27] chrXIII ? ? ?- ? 36M ? ? 36 804955 804990 ? ?36 ? ?0 >>>> [28] chrXIII ? ? ?- ? 36M ? ? 36 804974 805009 ? ?36 ? ?0 >>>>> exonRanges[6646] >>>> GRangesList of length 1 >>>> $6646 >>>> GRanges with 1 range and 3 elementMetadata values >>>> ? ?seqnames ? ? ? ? ? ranges strand | ? exon_id ? exon_name exon_rank >>>> ? ? ? <rle> ? ? ? ?<iranges> ?<rle> | <integer> <character> <integer> >>>> [1] ?chrXIII [804455, 805090] ? ? ?+ | ? ? ?7011 ? ? ? ? ?NA ? ? ? ? 1 >>>> >>>> >>>> seqlengths >>>> ? chrIV ? chrXV ?chrVII ?chrXII ?chrXVI ... ? chrVI ? ?chrI ? ?chrM 2micron >>>> ?1531919 1091289 1090947 1078175 ?948062 ... ?270148 ?230208 ? 85779 ? ?6318 >>>>> counts[6646] >>>> [1] 13 >>>>> table(strand(aligns[705:732])) >>>> >>>> ?+ ?- >>>> 13 15 >>>> >>>> >>>>> sessionInfo() >>>> R version 2.12.0 (2010-10-15) >>>> 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=C ? ? ? ? ? ? ?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] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>> >>>> other attached packages: >>>> [1] Rsamtools_1.2.1 ? ? ? Biostrings_2.18.0 ? ? GenomicFeatures_1.2.3 >>>> [4] GenomicRanges_1.2.1 ? IRanges_1.8.2 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.10.0 ? ? biomaRt_2.6.0 ? ? ?BSgenome_1.18.1 ? ?DBI_0.2-5 >>>> [5] RCurl_1.4-3 ? ? ? ?RSQLite_0.9-3 ? ? ?rtracklayer_1.10.5 tools_2.12.0 >>>> [9] XML_3.2-0 >>>> >>>> Song Li >>>> -- >>>> Postdoctoral Associate >>>> Institute for Genome Sciences and Policy >>>> Duke University >>>> >>>> _______________________________________________ >>>> 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 >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> > > > > -- > Postdoctoral Associate > Institute for Genome Sciences and Policy > Duke University >
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jason0701 ▴ 190
@jason0701-3921
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Song Li <songli116 at="" ...=""> writes: > > Hi Martin and Vincent, > > Thank you for your replies, here is my code: > > > strand(exonRanges)<-"*" > Error in `strand<-`(`*tmp*`, value = "*") : > replacement 'value' is not an AtomicList with the same elementLengths as 'x' > > > levels(strand(aligns))<-c('*','*','*') > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "strand<-", for > signature "GappedAlignments" > > It does not seem to be that straightforward. > > I have been searching for ways to make modification to the > GappedAlignments and GRangesList objects. > > Song > I just encountered the same problem. What I did is this aln <- grg(readBamGappedAlignments(bam)) strand(aln) = "*" countOverlaps(exonRanges, aln) Jason
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Hi Song, Vince, Martin, Jason, On 12/13/2010 11:22 AM, Jason wrote: [...] > > I just encountered the same problem. > What I did is this > > aln<- grg(readBamGappedAlignments(bam)) > strand(aln) = "*" > countOverlaps(exonRanges, aln) FWIW I just added a "strand<-" method for GappedAlignments objects to the devel version of the GenomicRanges package (1.3.7). From the (updated) man page for GappedAlignments: > subject GRanges with 1 range and 0 elementMetadata values seqnames ranges strand | <rle> <iranges> <rle> | [1] seq1 [1, 36] + | > galn[8:10] GappedAlignments of length 3 rname strand cigar qwidth start end width ngap [1] seq1 + 35M 35 15 49 35 0 [2] seq1 - 35M 35 18 52 35 0 [3] seq1 + 35M 35 22 56 35 0 > countOverlaps(galn[8:10], subject) [1] 1 0 1 > strand(galn) <- "*" > galn[8:10] GappedAlignments of length 3 rname strand cigar qwidth start end width ngap [1] seq1 * 35M 35 15 49 35 0 [2] seq1 * 35M 35 18 52 35 0 [3] seq1 * 35M 35 22 56 35 0 > countOverlaps(galn[8:10], subject) [1] 1 1 1 Just to clarify: because GappedAlignments objects follow the Samtools convention to provide CIGARs that are *always* relative to the + strand (even for alignments that are on the - strand), modifying the strand of a GappedAlignments object doesn't alter its cigar field (or any other field). Cheers, H. > sessionInfo() R version 2.13.0 Under development (unstable) (2010-11-28 r53696) Platform: x86_64-unknown-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=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.3.11 Biostrings_2.19.2 GenomicRanges_1.3.7 [4] IRanges_1.9.17 loaded via a namespace (and not attached): [1] Biobase_2.11.6 tools_2.13.0 > > > Jason > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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