[Bioc-devel] summarizeOverlaps example error
Mark Robinson
mark.robinson at imls.uzh.ch
Tue Aug 7 06:56:12 CEST 2012
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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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