[Bioc-devel] summarizeOverlaps example error
For what its worth, a colleague checked it out on a couple different systems (Thanks Keith!) and ? I don't think my original using R-devel instead of R-2.15.1 is really the issue. This works ? no error.
sessionInfo()
R Under development (unstable) (2012-06-11 r59557) 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=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] TxDb.Dmelanogaster.UCSC.dm3.ensGene_2.7.1 [2] GenomicFeatures_1.9.11 [3] AnnotationDbi_1.19.16 [4] BiocInstaller_1.5.12 [5] edgeR_2.7.25 [6] limma_3.13.8 [7] DESeq_1.9.7 [8] locfit_1.5-8 [9] Biobase_2.17.6 [10] Rsamtools_1.9.18 [11] Biostrings_2.25.6 [12] GenomicRanges_1.9.28 [13] IRanges_1.15.17 [14] BiocGenerics_0.3.0 loaded via a namespace (and not attached): [1] annotate_1.35.3 biomaRt_2.13.1 bitops_1.0-4.1 [4] BSgenome_1.25.3 DBI_0.2-5 genefilter_1.39.0 [7] geneplotter_1.35.0 grid_2.16.0 lattice_0.20-6 [10] RColorBrewer_1.0-5 RCurl_1.91-1 RSQLite_0.11.1 [13] rtracklayer_1.17.11 splines_2.16.0 stats4_2.16.0 [16] survival_2.36-14 tools_2.16.0 XML_3.9-4 [19] xtable_1.7-0 zlibbioc_1.3.0
This throws the same error as mine ?
sessionInfo()
R Under development (unstable) (2012-05-08 r59331) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TxDb.Dmelanogaster.UCSC.dm3.ensGene_2.7.1 [2] GenomicFeatures_1.9.28 [3] AnnotationDbi_1.19.28 [4] edgeR_2.99.4 [5] limma_3.13.16 [6] DESeq_1.9.11 [7] lattice_0.20-6 [8] locfit_1.5-8 [9] Biobase_2.17.6 [10] Rsamtools_1.9.25 [11] Biostrings_2.25.8 [12] GenomicRanges_1.9.41 [13] IRanges_1.15.25 [14] BiocGenerics_0.3.0 [15] BiocInstaller_1.5.12 loaded via a namespace (and not attached): [1] annotate_1.35.3 biomaRt_2.13.2 bitops_1.0-4.1 [4] BSgenome_1.25.6 DBI_0.2-5 genefilter_1.39.0 [7] geneplotter_1.35.1 grid_2.16.0 RColorBrewer_1.0-5 [10] RCurl_1.91-1.1 RSQLite_0.11.1 rtracklayer_1.17.15 [13] splines_2.16.0 stats4_2.16.0 survival_2.36-14 [16] tools_2.16.0 XML_3.9-4.1 xtable_1.7-0 [19] zlibbioc_1.3.0
So, something has happened between GenomicRanges_1.9.28 and GenomicRanges_1.9.41 (plus a multitude other changes). Best, Mark
On 06.08.2012, at 22:11, Dan Tenenbaum wrote:
Hi Mark, On Mon, Aug 6, 2012 at 1:01 PM, Mark Robinson <mark.robinson at imls.uzh.ch> wrote:
Hi all, My apologies in advance if I've done something pin-headed here, but can anyone else produce an error just by doing: library(GenomicRanges) example(summarizeOverlaps) I think I have a set of updated (devel) packages:
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.5.12, ?biocLite for help
old.packages(repos=biocinstallRepos())
NULL My R devel is a bit old (2012-06-14 r59564) ? maybe I should upgrade?
The devel version of Bioconductor (2.11) is not intended for use with R-devel. It's meant to be used with R 2.15 (just as Bioconductor 2.10, the release version, is). It's a bit confusing. It's because R moved to a yearly release schedule but we are keeping our twice-yearly release schedule. I don't know if that is the cause of your problems, but Bioconductor packages are not tested or built on R-devel, so who knows what could happen. Unless there is some feature in R-devel that you really want, I'd suggest trying R 2.15 and see if that fixes things. More info here: http://bioconductor.org/developers/useDevel/ Dan
Error, traceback() and sessionInfo() below ? Help much appreciated. Best, Mark
example(summarizeOverlaps)
smmrzO> reads <- GappedAlignments(
smmrzO+ names = c("a","b","c","d","e","f","g"),
smmrzO+ seqnames = Rle(c(rep(c("chr1", "chr2"), 3), "chr1")),
smmrzO+ pos = as.integer(c(1400, 2700, 3400, 7100, 4000, 3100, 5200)),
smmrzO+ cigar = c("500M", "100M", "300M", "500M", "300M",
smmrzO+ "50M200N50M", "50M150N50M"),
smmrzO+ strand = strand(rep("+", 7)))
smmrzO> ## ---------------------------------------------------------------------
smmrzO> ## 'features' as GRanges
smmrzO> ##
smmrzO>
smmrzO> features <- GRanges(
smmrzO+ seqnames = c(rep("chr1", 7), rep("chr2", 4)), strand = "+",
smmrzO+ ranges = IRanges(c(1000, 3000, 3600, 4000, 4000, 5000, 5400, 2000,
smmrzO+ 3000, 7000, 7500), width = c(500, 500, 300, 500, 900, 500, 500,
smmrzO+ 900, 500, 600, 300)),
smmrzO+ group_id = c("A", "B", "C", "C", "D", "D", "E", "F", "G", "H", "H"))
smmrzO> ## Each row is a feature the read can 'hit'.
smmrzO> rowsAsFeatures <- data.frame(
smmrzO+ union = assays(summarizeOverlaps(features, reads))$counts,
smmrzO+ intStrict = assays(summarizeOverlaps(features, reads,
smmrzO+ mode="IntersectionStrict"))$counts,
smmrzO+ intNotEmpty = assays(summarizeOverlaps(features, reads,
smmrzO+ mode="IntersectionNotEmpty"))$counts,
smmrzO+ countOverlaps = countOverlaps(features, reads))
smmrzO> ## Results from countOverlaps() are included to highlight how
smmrzO> ## summarizeOverlaps() counts a read only once. For these 7
smmrzO> ## reads, 'Union' is the most conservative counting mode, followed
smmrzO> ## by 'Intersectionstrict' and then 'IntersectionNotEmpty'.
smmrzO>
smmrzO> colSums(rowsAsFeatures)
union intStrict intNotEmpty countOverlaps
3 4 5 11
smmrzO> ## ---------------------------------------------------------------------
smmrzO> ## 'features' as GRangesList
smmrzO> ##
smmrzO>
smmrzO> ## Each highest list-level is a feature the read can 'hit'.
smmrzO> lst <- split(features, values(features)[["group_id"]])
smmrzO> listAsFeatures <- data.frame(
smmrzO+ union = assays(summarizeOverlaps(lst, reads))$counts,
smmrzO+ intStrict = assays(summarizeOverlaps(lst, reads,
smmrzO+ mode="IntersectionStrict"))$counts,
smmrzO+ intNotEmpty = assays(summarizeOverlaps(lst, reads,
smmrzO+ mode="IntersectionNotEmpty"))$counts,
smmrzO+ countOverlaps = countOverlaps(lst, reads))
smmrzO> ## ---------------------------------------------------------------------
smmrzO> ## 'reads' as BamFileList
smmrzO> ##
smmrzO>
smmrzO> ## Count BAM files and prepare output for DESeq or edgeR analysis
smmrzO> library(Rsamtools)
smmrzO> library(DESeq)
smmrzO> library(edgeR)
smmrzO> fls <- list.files(system.file("extdata",package="GenomicRanges"),
smmrzO+ recursive=TRUE, pattern="*bam$", full=TRUE)
smmrzO> names(fls) <- basename(fls)
smmrzO> bfl <- BamFileList(fls, index=character())
smmrzO> features <- GRanges(
smmrzO+ seqnames = c(rep("chr2L", 4), rep("chr2R", 5), rep("chr3L", 2)),
smmrzO+ ranges = IRanges(c(1000, 3000, 4000, 7000, 2000, 3000, 3600, 4000,
smmrzO+ 7500, 5000, 5400), width=c(rep(500, 3), 600, 900, 500, 300, 900,
smmrzO+ 300, 500, 500)), "-",
smmrzO+ group_id=c(rep("A", 4), rep("B", 5), rep("C", 2)))
smmrzO> solap <- summarizeOverlaps(features, bfl)
smmrzO> deseq <- newCountDataSet(assays(solap)$counts, rownames(colData(solap)))
smmrzO> edger <- DGEList(assays(solap)$counts, group=rownames(colData(solap)))
Calculating library sizes from column totals.
smmrzO> ## ---------------------------------------------------------------------
smmrzO> ## paired-end reads
smmrzO> ##
smmrzO>
smmrzO> library("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
smmrzO> exbygene <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene")
smmrzO> fl <- system.file("extdata", "untreated3_chr4.bam",
smmrzO+ package="pasillaBamSubset")
smmrzO> ## Paired-end reads are stored in a GappedAlignmentPairs object
smmrzO> reads <- readGappedAlignmentPairs(fl)
smmrzO> res <- summarizeOverlaps(exbygene, reads, "Union")
Warning messages:
1: In is.na(unique(f)) :
is.na() applied to non-(list or vector) of type 'S4'
2: In IRanges:::newCompressedList("GRangesList", x, splitFactor = f, :
data length is not a multiple of split variable
Error in countOverlaps(reads, features, ignore.strand = ignore.strand) :
error in evaluating the argument 'query' in selecting a method for function 'countOverlaps': Error in unique.default(x) : unique() applies only to vectors
traceback()
10: countOverlaps(reads, features, ignore.strand = ignore.strand)
9: mode(reads, features, ignore.strand)
8: .dispatchOverlaps(grglist(reads), features, mode, ignore.strand)
7: summarizeOverlaps(exbygene, reads, "Union")
6: summarizeOverlaps(exbygene, reads, "Union") at Rex84b25fb6afa1#102
5: eval(expr, envir, enclos)
4: eval(ei, envir)
3: withVisible(eval(ei, envir))
2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
getOption("prompt")), continue.echo = paste0(prompt.prefix,
getOption("continue")), verbose = verbose, max.deparse.length = Inf,
encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
1: example(summarizeOverlaps)
sessionInfo()
R Under development (unstable) (2012-06-14 r59564) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.5.12 [2] TxDb.Dmelanogaster.UCSC.dm3.ensGene_2.7.1 [3] GenomicFeatures_1.9.28 [4] AnnotationDbi_1.19.28 [5] edgeR_2.99.4 [6] limma_3.13.16 [7] DESeq_1.9.11 [8] lattice_0.20-6 [9] locfit_1.5-8 [10] Biobase_2.17.6 [11] Rsamtools_1.9.25 [12] Biostrings_2.25.8 [13] GenomicRanges_1.9.41 [14] IRanges_1.15.25 [15] BiocGenerics_0.3.0 loaded via a namespace (and not attached): [1] annotate_1.35.3 biomaRt_2.13.2 bitops_1.0-4.1 [4] BSgenome_1.25.6 DBI_0.2-5 genefilter_1.39.0 [7] geneplotter_1.35.1 grid_2.16.0 RColorBrewer_1.0-5 [10] RCurl_1.91-1 RSQLite_0.11.1 rtracklayer_1.17.15 [13] splines_2.16.0 stats4_2.16.0 survival_2.36-14 [16] tools_2.16.0 XML_3.9-4 xtable_1.7-0 [19] zlibbioc_1.3.0
---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson at imls.uzh.ch o: Y11-J-16 w: http://tiny.cc/mrobin ---------- http://www.fgcz.ch/Bioconductor2012 http://www.eccb12.org/t5
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