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Question: IRanges: the width argument of the coverage function
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gravatar for delhomme@embl.de
4.8 years ago by
delhomme@embl.de1.2k wrote:
Hi, I thought I saw a mention on the mailing list that coverage and similar functions would support a named vector for providing the width instead of just a list. The documentation states so too: For RangesList and RangedData objects, a list or vector of the same length as ?x? to be used for the corresponding element in ?x?. However, using a named vector does not work (my aln.ranges is a RangesList object): > class(aln.ranges) [1] "CompressedIRangesList" attr(,"package") [1] "IRanges" > coverage(aln.ranges,width=chrSize(obj)) Error in .local(x, shift, width, weight, ...) : 'width' must be a non-empty list > str(chrSize(obj)) # that's my width Named int [1:2518] 48367220 21538349 8012 10863 7999 7999 7991 8236 7962 8324 ... - attr(*, "names")= chr [1:2518] "scaffold_1" "scaffold_10" "scaffold_1000" "scaffold_1001" ... Changing the width to a list works: > coverage(aln.ranges,width=as.list(chrSize(obj))) So, I'm just curious what the status is. Thanks, Nico > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] easyRNASeq_1.3.6 ShortRead_1.15.9 latticeExtra_0.6-19 [4] RColorBrewer_1.0-5 lattice_0.20-6 Rsamtools_1.9.18 [7] DESeq_1.9.7 locfit_1.5-8 BSgenome_1.25.3 [10] GenomicRanges_1.9.28 Biostrings_2.25.6 edgeR_2.7.24 [13] limma_3.13.7 biomaRt_2.13.1 Biobase_2.17.6 [16] genomeIntervals_1.13.2 intervals_0.13.3 IRanges_1.15.17 [19] BiocGenerics_0.3.0 loaded via a namespace (and not attached): [1] annotate_1.35.3 AnnotationDbi_1.19.15 bitops_1.0-4.1 [4] DBI_0.2-5 genefilter_1.39.0 geneplotter_1.35.0 [7] grid_2.15.1 hwriter_1.3 RCurl_1.91-1 [10] RSQLite_0.11.1 splines_2.15.1 stats4_2.15.1 [13] survival_2.36-14 tools_2.15.1 XML_3.9-4 [16] xtable_1.7-0 zlibbioc_1.3.0 --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany
ADD COMMENTlink modified 4.8 years ago by Hervé Pagès ♦♦ 12k • written 4.8 years ago by delhomme@embl.de1.2k
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gravatar for Hervé Pagès
4.8 years ago by
Hervé Pagès ♦♦ 12k
United States
Hervé Pagès ♦♦ 12k wrote:
Hi Nico, On 07/03/2012 07:39 AM, Nicolas Delhomme wrote: > Hi, > > I thought I saw a mention on the mailing list that coverage and similar functions would support a named vector for providing the width instead of just a list. The documentation states so too: > Mmmh, I thought so too. But apparently this works for GRanges objects but not for RangesList objects. > For RangesList and RangedData objects, a list or vector of > the same length as ?x? to be used for the corresponding > element in ?x?. > > However, using a named vector does not work (my aln.ranges is a RangesList object): > >> class(aln.ranges) > [1] "CompressedIRangesList" > attr(,"package") > [1] "IRanges" > >> coverage(aln.ranges,width=chrSize(obj)) > Error in .local(x, shift, width, weight, ...) : > 'width' must be a non-empty list > >> str(chrSize(obj)) # that's my width > Named int [1:2518] 48367220 21538349 8012 10863 7999 7999 7991 8236 7962 8324 ... > - attr(*, "names")= chr [1:2518] "scaffold_1" "scaffold_10" "scaffold_1000" "scaffold_1001" ... > > Changing the width to a list works: >> coverage(aln.ranges,width=as.list(chrSize(obj))) > > So, I'm just curious what the status is. Will fix the "coverage" method for RangesList (and its man page) so it's consistent with the method for GRanges. Thanks, H. > > Thanks, > > Nico > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] easyRNASeq_1.3.6 ShortRead_1.15.9 latticeExtra_0.6-19 > [4] RColorBrewer_1.0-5 lattice_0.20-6 Rsamtools_1.9.18 > [7] DESeq_1.9.7 locfit_1.5-8 BSgenome_1.25.3 > [10] GenomicRanges_1.9.28 Biostrings_2.25.6 edgeR_2.7.24 > [13] limma_3.13.7 biomaRt_2.13.1 Biobase_2.17.6 > [16] genomeIntervals_1.13.2 intervals_0.13.3 IRanges_1.15.17 > [19] BiocGenerics_0.3.0 > > loaded via a namespace (and not attached): > [1] annotate_1.35.3 AnnotationDbi_1.19.15 bitops_1.0-4.1 > [4] DBI_0.2-5 genefilter_1.39.0 geneplotter_1.35.0 > [7] grid_2.15.1 hwriter_1.3 RCurl_1.91-1 > [10] RSQLite_0.11.1 splines_2.15.1 stats4_2.15.1 > [13] survival_2.36-14 tools_2.15.1 XML_3.9-4 > [16] xtable_1.7-0 zlibbioc_1.3.0 > > > --------------------------------------------------------------- > Nicolas Delhomme > > Genome Biology Computational Support > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: nicolas.delhomme at embl.de > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > > _______________________________________________ > 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, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 4.8 years ago by Hervé Pagès ♦♦ 12k
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