hi,
VariantAnnotation::locateVariants() is breaking in a very specific way
in its current devel version (1.13.26). Since I'm using it while working
on VariantFiltering, I have reverted my copy of VariantAnnotation to
version 1.13.24 to be able to continue working.
so at the moment this is not much of a problem for me, but I thought you
might be interested in knowing about it, just in case you were not aware
of it. This is the minimal example I've come up reproducing it:
library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
gr <- GRanges(rep("chr20", 1), IRanges(start=44501458, width=1))
loc <- locateVariants(gr, txdb,
AllVariants(intergenic=IntergenicVariants(0, 0)))
Error in .Primitive("c")(<S4 object of class "CompressedIntegerList">, :
all arguments in '...' must be CompressedList objects
traceback()
traceback()
23: stop("all arguments in '...' must be CompressedList objects")
22: .Primitive("c")(<S4 object of class "CompressedIntegerList">,
NA_integer_)
21: .Primitive("c")(<S4 object of class "CompressedIntegerList">,
NA_integer_)
20: do.call(c, unname(cols))
19: do.call(c, unname(cols))
18: FUN(c("LOCATION", "LOCSTART", "LOCEND", "QUERYID", "TXID", "CDSID",
"GENEID", "PRECEDEID", "FOLLOWID")[[6L]], ...)
17: lapply(colnames(df), function(cn) {
cols <- lapply(args, `[[`, cn)
isRle <- vapply(cols, is, logical(1L), "Rle")
if (any(isRle) && !all(isRle)) {
cols[isRle] <- lapply(cols[isRle], S4Vectors:::decodeRle)
}
isFactor <- vapply(cols, is.factor, logical(1L))
if (any(isFactor)) {
cols <- lapply(cols, as.factor)
levs <- unique(unlist(lapply(cols, levels), use.names =
FALSE))
cols <- lapply(cols, factor, levs)
}
rectangular <- length(dim(cols[[1]])) == 2L
if (rectangular) {
combined <- do.call(rbind, unname(cols))
}
else {
combined <- do.call(c, unname(cols))
}
if (any(isFactor))
combined <- structure(combined, class = "factor", levels =
levs)
combined
})
16: lapply(colnames(df), function(cn) {
cols <- lapply(args, `[[`, cn)
isRle <- vapply(cols, is, logical(1L), "Rle")
if (any(isRle) && !all(isRle)) {
cols[isRle] <- lapply(cols[isRle], S4Vectors:::decodeRle)
}
isFactor <- vapply(cols, is.factor, logical(1L))
if (any(isFactor)) {
cols <- lapply(cols, as.factor)
levs <- unique(unlist(lapply(cols, levels), use.names =
FALSE))
cols <- lapply(cols, factor, levs)
}
rectangular <- length(dim(cols[[1]])) == 2L
if (rectangular) {
combined <- do.call(rbind, unname(cols))
}
else {
combined <- do.call(c, unname(cols))
}
if (any(isFactor))
combined <- structure(combined, class = "factor", levels =
levs)
combined
})
15: .Method(..., deparse.level = deparse.level)
14: eval(expr, envir, enclos)
13: eval(.dotsCall, env)
12: eval(.dotsCall, env)
11: standardGeneric("rbind")
10: (function (..., deparse.level = 1)
standardGeneric("rbind"))(<S4 object of class "DataFrame">, <S4
object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class
"DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class
"DataFrame">,
<S4 object of class "DataFrame">)
9: do.call(rbind, lapply(x, mcols, FALSE))
8: do.call(rbind, lapply(x, mcols, FALSE))
7: .unlist_list_of_GenomicRanges(args, ignore.mcols = ignore.mcols)
6: .local(x, ..., recursive = recursive)
5: c(coding, intron, fiveUTR, threeUTR, splice, promoter, intergenic)
4: c(coding, intron, fiveUTR, threeUTR, splice, promoter, intergenic)
3: .local(query, subject, region, ...)
2: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
0)))
1: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
0)))
interestingly, if i replace the chromosome name in the GRanges object of
'chr20' by 'chr2', then it works:
gr <- GRanges(rep("chr2", 1), IRanges(start=44501458, width=1))
loc <- locateVariants(gr, txdb,
AllVariants(intergenic=IntergenicVariants(0, 0)))
or if i replace the start of the ranges of 44501458 by 1, then it also
works:
gr <- GRanges(rep("chr20", 1), IRanges(start=1, width=1))
loc <- locateVariants(gr, txdb,
AllVariants(intergenic=IntergenicVariants(0, 0)))
here is the sessionInfo():
R Under development (unstable) (2014-10-14 r66765)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.17
AnnotationDbi_1.29.17
[4] Biobase_2.27.1 VariantAnnotation_1.13.26
Rsamtools_1.19.26
[7] Biostrings_2.35.7 XVector_0.7.3
GenomicRanges_1.19.35
[10] GenomeInfoDb_1.3.12 IRanges_2.1.36
S4Vectors_0.5.17
[13] BiocGenerics_0.13.4 vimcom_1.0-0
setwidth_1.0-3
[16] colorout_1.0-3
loaded via a namespace (and not attached):
[1] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8
BiocParallel_1.1.13 biomaRt_2.23.5
[6] bitops_1.0-6 brew_1.0-6 BSgenome_1.35.16
checkmate_1.5.1 codetools_0.2-10
[11] DBI_0.3.1 digest_0.6.8 fail_1.2
foreach_1.4.2 GenomicAlignments_1.3.27
[16] iterators_1.0.7 RCurl_1.95-4.5 RSQLite_1.0.0
rtracklayer_1.27.7 sendmailR_1.2-1
[21] stringr_0.6.2 tools_3.2.0 XML_3.98-1.1
zlibbioc_1.13.0
this problem dissapear if i revert to the older version (1.13.24),
svn merge -r 98874:98522 .
build and install it. in a new fresh R-devel session the same code
smoothly with some warnings, i believe unrelated to this problem:
[...]
loc <- locateVariants(gr, txdb,
+ AllVariants(intergenic=IntergenicVariants(0, 0)))
Warning messages:
1: '.local' is deprecated.
Use 'mapToTranscripts' instead.
See help("Deprecated")
2: '.local' is deprecated.
Use 'mapToTranscripts' instead.
See help("Deprecated")
3: '.local' is deprecated.
Use 'mapToTranscripts' instead.
See help("Deprecated")
4: '.local' is deprecated.
Use 'mapToTranscripts' instead.
See help("Deprecated")
this is the sessionInfo() of this run:
R Under development (unstable) (2014-10-14 r66765)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
LC_COLLATE=en_US.UTF8
[5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
LC_PAPER=en_US.UTF8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.17
AnnotationDbi_1.29.17
[4] Biobase_2.27.1 VariantAnnotation_1.13.24
Rsamtools_1.19.26
[7] Biostrings_2.35.7 XVector_0.7.3
GenomicRanges_1.19.35
[10] GenomeInfoDb_1.3.12 IRanges_2.1.36
S4Vectors_0.5.17
[13] BiocGenerics_0.13.4 vimcom_1.0-0
setwidth_1.0-3
[16] colorout_1.0-3
loaded via a namespace (and not attached):
[1] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8
BiocParallel_1.1.13 biomaRt_2.23.5
[6] bitops_1.0-6 brew_1.0-6 BSgenome_1.35.16
checkmate_1.5.1 codetools_0.2-10
[11] DBI_0.3.1 digest_0.6.8 fail_1.2
foreach_1.4.2 GenomicAlignments_1.3.27
[16] iterators_1.0.7 RCurl_1.95-4.5 RSQLite_1.0.0
rtracklayer_1.27.7 sendmailR_1.2-1
[21] stringr_0.6.2 tools_3.2.0 XML_3.98-1.1
zlibbioc_1.13.0
cheers,
robert.
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