RleList
1
1
Entering edit mode
@massimo-petretich-6303
Last seen 7.0 years ago
Dear All, I am a hard time converting a list of Rle to a RleList. The very same code was working fine with R 2.15.2 and IRanges 1.17.1. > BAM<-readAligned(dirPath=directory, pattern=paste("srtRmdup_",tag, > ".bam",sep=""), type="BAM") > lc <- BAM[ !is.na(chromosome(BAM))] > cvg <- coverage(lc, extend=eval(parse(text=paste(fragmentSize,"L", > sep="")))-width(lc)) > y<-mclapply(cvg[sapply(cvg, length)>3*window], smoothRle, > window=window, resolution=resolution, mc.cores=cores) > head(y,2) $chr1 numeric-Rle of length 197195000 with 191252 runs Lengths: 2990000 1000 ... 10000 Values : 0 35.7142857142857 ... 1068.71428571429 $chr2 numeric-Rle of length 181748000 with 178193 runs Lengths: 2990000 1000 ... 11000 Values : 0 15.3809523809524 ... 1286.85714285714 > y<-RleList(y) Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "IRanges") : integer overflow while summing elements in 'lengths' # It gives the same error if I convert an RleList to list and then back to RleList: > cvg RleList of length 35 $chr1 integer-Rle of length 197195057 with 2181706 runs Lengths: 3000467 2 27 221 ... 98 21 400 250 Values : 0 1 2 3 ... 2 1 0 1 $chr2 integer-Rle of length 181748164 with 2182776 runs Lengths: 3000128 250 549 99 ... 51 9 48 54 Values : 0 1 0 1 ... 4 3 2 1 $chr3 integer-Rle of length 159599909 with 1760167 runs Lengths: 2999875 250 6 123 ... 22 136 114 136 Values : 0 1 0 1 ... 0 1 2 1 $chr4 integer-Rle of length 155630246 with 1888170 runs Lengths: 3000290 250 229 250 ... 5 92 111 47 Values : 0 1 0 1 ... 2 3 2 1 $chr5 integer-Rle of length 152537402 with 1759560 runs Lengths: 2999987 250 490 196 ... 9 133 14 8 Values : 0 1 0 1 ... 4 3 2 1 ... <30 more elements> > cvgLst <- as.list(cvg) > cvg <- RleList(cvgLst) Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "IRanges") : integer overflow while summing elements in 'lengths' # The problem isn't likely the data itself or the syntax, > cvg<-RleList(cvgLst[1:10]) > cvg RleList of length 10 $chr1 integer-Rle of length 197195057 with 2181706 runs Lengths: 3000467 2 27 221 ... 98 21 400 250 Values : 0 1 2 3 ... 2 1 0 1 $chr2 integer-Rle of length 181748164 with 2182776 runs Lengths: 3000128 250 549 99 ... 51 9 48 54 Values : 0 1 0 1 ... 4 3 2 1 $chr3 integer-Rle of length 159599909 with 1760167 runs Lengths: 2999875 250 6 123 ... 22 136 114 136 Values : 0 1 0 1 ... 0 1 2 1 $chr4 integer-Rle of length 155630246 with 1888170 runs Lengths: 3000290 250 229 250 ... 5 92 111 47 Values : 0 1 0 1 ... 2 3 2 1 $chr5 integer-Rle of length 152537402 with 1759560 runs Lengths: 2999987 250 490 196 ... 9 133 14 8 Values : 0 1 0 1 ... 4 3 2 1 ... <5 more elements> > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=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] MALDIquant_1.8 rtracklayer_1.22.0 ShortRead_1.20.0 [4] Rsamtools_1.14.2 lattice_0.20-24 Biostrings_2.30.1 [7] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 [10] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] Biobase_2.22.0 bitops_1.0-6 BSgenome_1.30.0 [4] grid_3.0.2 hwriter_1.3 latticeExtra_0.6-26 [7] RColorBrewer_1.0-5 RCurl_1.95-4.1 stats4_3.0.2 [10] tools_3.0.2 XML_3.98-1.1 zlibbioc_1.8.0 Perhaps I am unaware of some changes introduced in the latest version of IRanges that make this operation not possible, I hope somebody has some suggestions to give me. Thanks and best regards, Massimo
convert IRanges convert IRanges • 1.5k views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-3846
Last seen 6 weeks ago
United States
You need RleList(x, compress=FALSE) for cases when sum(elementLengths(x)) exceeds 2^32. The default value of that argument was changed to TRUE last release cycle. Michael On Tue, Dec 24, 2013 at 2:59 AM, Massimo Petretich <petretic@embl.de> wrote: > Dear All, > > I am a hard time converting a list of Rle to a RleList. > The very same code was working fine with R 2.15.2 and IRanges 1.17.1. > > > > BAM<-readAligned(dirPath=directory, pattern=paste("srtRmdup_",tag, >> ".bam",sep=""), type="BAM") >> > > lc <- BAM[ !is.na(chromosome(BAM))] >> > > cvg <- coverage(lc, extend=eval(parse(text=paste(fragmentSize,"L", >> sep="")))-width(lc)) >> > > y<-mclapply(cvg[sapply(cvg, length)>3*window], smoothRle, window=window, >> resolution=resolution, mc.cores=cores) >> > > head(y,2) >> > $chr1 > numeric-Rle of length 197195000 with 191252 runs > Lengths: 2990000 1000 ... 10000 > Values : 0 35.7142857142857 ... 1068.71428571429 > > $chr2 > numeric-Rle of length 181748000 with 178193 runs > Lengths: 2990000 1000 ... 11000 > Values : 0 15.3809523809524 ... 1286.85714285714 > > y<-RleList(y) >> > Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = > "IRanges") : > integer overflow while summing elements in 'lengths' > > > > # It gives the same error if I convert an RleList to list and then back to > RleList: > > > cvg >> > RleList of length 35 > $chr1 > integer-Rle of length 197195057 with 2181706 runs > Lengths: 3000467 2 27 221 ... 98 21 400 > 250 > Values : 0 1 2 3 ... 2 1 0 > 1 > > $chr2 > integer-Rle of length 181748164 with 2182776 runs > Lengths: 3000128 250 549 99 ... 51 9 48 > 54 > Values : 0 1 0 1 ... 4 3 2 > 1 > > $chr3 > integer-Rle of length 159599909 with 1760167 runs > Lengths: 2999875 250 6 123 ... 22 136 114 > 136 > Values : 0 1 0 1 ... 0 1 2 > 1 > > $chr4 > integer-Rle of length 155630246 with 1888170 runs > Lengths: 3000290 250 229 250 ... 5 92 111 > 47 > Values : 0 1 0 1 ... 2 3 2 > 1 > > $chr5 > integer-Rle of length 152537402 with 1759560 runs > Lengths: 2999987 250 490 196 ... 9 133 14 > 8 > Values : 0 1 0 1 ... 4 3 2 > 1 > ... > <30 more elements> > > > cvgLst <- as.list(cvg) >> > > cvg <- RleList(cvgLst) >> > Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = > "IRanges") : > integer overflow while summing elements in 'lengths' > > > # The problem isn't likely the data itself or the syntax, > >> cvg<-RleList(cvgLst[1:10]) >> > > cvg >> > RleList of length 10 > $chr1 > integer-Rle of length 197195057 with 2181706 runs > Lengths: 3000467 2 27 221 ... 98 21 400 > 250 > Values : 0 1 2 3 ... 2 1 0 > 1 > > $chr2 > integer-Rle of length 181748164 with 2182776 runs > Lengths: 3000128 250 549 99 ... 51 9 48 > 54 > Values : 0 1 0 1 ... 4 3 2 > 1 > > $chr3 > integer-Rle of length 159599909 with 1760167 runs > Lengths: 2999875 250 6 123 ... 22 136 114 > 136 > Values : 0 1 0 1 ... 0 1 2 > 1 > > $chr4 > integer-Rle of length 155630246 with 1888170 runs > Lengths: 3000290 250 229 250 ... 5 92 111 > 47 > Values : 0 1 0 1 ... 2 3 2 > 1 > > $chr5 > integer-Rle of length 152537402 with 1759560 runs > Lengths: 2999987 250 490 196 ... 9 133 14 > 8 > Values : 0 1 0 1 ... 4 3 2 > 1 > ... > <5 more elements> > > > sessionInfo() >> > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=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] MALDIquant_1.8 rtracklayer_1.22.0 ShortRead_1.20.0 > [4] Rsamtools_1.14.2 lattice_0.20-24 Biostrings_2.30.1 > [7] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 > [10] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.22.0 bitops_1.0-6 BSgenome_1.30.0 > [4] grid_3.0.2 hwriter_1.3 latticeExtra_0.6-26 > [7] RColorBrewer_1.0-5 RCurl_1.95-4.1 stats4_3.0.2 > [10] tools_3.0.2 XML_3.98-1.1 zlibbioc_1.8.0 > > > > > Perhaps I am unaware of some changes introduced in the latest version of > IRanges > that make this operation not possible, > I hope somebody has some suggestions to give me. > > Thanks and best regards, > Massimo > > _______________________________________________ > 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]]
ADD COMMENT

Login before adding your answer.

Traffic: 159 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6