[Bioc-devel] summarizeOverlaps example error

res

sessionInfo()

Hi Mark,

Try GenomicRanges 1.9.42 which requires IRanges 1.15.29. The example ran successfully for me with this combination. There was a problem was with newCompressedList() in IRanges which was fixed in r68298.

Valerie

svn log for IRanges :

------------------------------------------------------------------------
r68298 | hpages at fhcrc.org | 2012-08-07 18:43:15 -0700 (Tue, 07 Aug 2012) | 3 lines

Small tweak to newCompressedList0() internal constructor so it produces valid
GRangesList objects.




On 08/06/12 21:56, Mark Robinson wrote:

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

----------
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