hi Valerie,
thanks for the fix, it seems that it required a more complex update than
i initially thought looking at the code. actually, i found out that this
update is breaking with the sample VCF file from the VariantFiltering
package. i guess this requires some further fix in VariantAnnotation.
The problem shows up in both, devel and release, please find at the
bottom both sessionInfo() outputs.
thanks!!
robert.
library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
fl <- system.file("extdata", "CEUtrio.vcf.bgz", package="VariantFiltering")
vcf <- readVcf(fl, genome="hg19")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
seqlevelsStyle(vcf) <- seqlevelsStyle(txdb)
## this is necessary to avoid the chrM length glitch between
## b37 (GATK bundle 2.8 reference genome) and hg19 versions
commonlev <- intersect(seqlevels(vcf), seqlevels(txdb))
commonlev <- commonlev[seqlengths(vcf)[commonlev] ==
seqlengths(txdb)[commonlev]]
vcf <- keepSeqlevels(vcf, commonlev)
loc_intron <- locateVariants(vcf, txdb, region=IntronVariants())
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains NAs or out-of-bounds indices
traceback()
27: stop("subscript contains NAs or out-of-bounds indices")
26: NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
25: NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
24: normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
23: extractROWS(x, i)
22: extractROWS(x, i)
21: ss[txHits]
20: ss[txHits]
19: is(strand, "Rle")
18: newGRanges("GRanges", seqnames = seqnames, ranges = ranges, strand =
strand,
mcols = DataFrame(...), seqlengths = seqlengths, seqinfo =
seqinfo)
17: GRanges(seqnames = seqnames(query)[xHits], ranges =
IRanges(ranges(query)[xHits]),
strand = ss[txHits], LOCATION = .location(length(xHits),
vtype), LOCSTART = start(map), LOCEND = end(map), QUERYID =
xHits,
TXID = txid, CDSID = cdsid, GENEID = NA_character_, PRECEDEID =
CharacterList(character(0)),
FOLLOWID = CharacterList(character(0)))
16: .makeResult(query, subject, "intron", ignore.strand = ignore.strand,
asHits = asHits)
15: .local(query, subject, region, ...)
14: locateVariants(query, cache[["intbytx"]], region, ..., ignore.strand
= ignore.strand,
asHits = asHits)
13: locateVariants(query, cache[["intbytx"]], region, ..., ignore.strand
= ignore.strand,
asHits = asHits)
12: eval(expr, envir, enclos)
11: eval(call, parent.frame())
10: callGeneric(query, cache[["intbytx"]], region, ..., ignore.strand =
ignore.strand,
asHits = asHits)
9: .local(query, subject, region, ...)
8: locateVariants(rowRanges(query), subject, region, ..., cache = cache,
ignore.strand = ignore.strand, asHits = asHits)
7: locateVariants(rowRanges(query), subject, region, ..., cache = cache,
ignore.strand = ignore.strand, asHits = asHits)
6: eval(expr, envir, enclos)
5: eval(call, parent.frame())
4: callGeneric(rowRanges(query), subject, region, ..., cache = cache,
ignore.strand = ignore.strand, asHits = asHits)
3: .local(query, subject, region, ...)
2: locateVariants(vcf, txdb, region = IntronVariants())
1: locateVariants(vcf, txdb, region = IntronVariants())
R Under development (unstable) (2015-04-28 r68268)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
[4] LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C LC_ADDRESS=C
[10] 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_3.1.3 GenomicFeatures_1.21.12
[3] AnnotationDbi_1.31.14 VariantAnnotation_1.15.11
[5] Rsamtools_1.21.8 Biostrings_2.37.2
[7] XVector_0.9.1 SummarizedExperiment_0.1.5
[9] Biobase_2.29.1 GenomicRanges_1.21.14
[11] GenomeInfoDb_1.5.7 IRanges_2.3.10
[13] S4Vectors_0.7.3 BiocGenerics_0.15.2
[15] vimcom_1.0-0 setwidth_1.0-3
[17] colorout_1.0-3
loaded via a namespace (and not attached):
[1] GenomicAlignments_1.5.9 zlibbioc_1.15.0 BiocParallel_1.3.22
BSgenome_1.37.1
[5] tools_3.3.0 DBI_0.3.1 lambda.r_1.1.7
futile.logger_1.4.1
[9] rtracklayer_1.29.7 futile.options_1.0.0 bitops_1.0-6
RCurl_1.95-4.6
[13] biomaRt_2.25.1 RSQLite_1.0.0 XML_3.98-1.2
*** SESSION INFORMATION FOR RELEASE ******
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora release 12 (Constantine)
locale:
[1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
[4] LC_COLLATE=en_US.UTF8 LC_MONETARY=en_US.UTF8
LC_MESSAGES=en_US.UTF8
[7] LC_PAPER=en_US.UTF8 LC_NAME=C LC_ADDRESS=C
[10] 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_3.1.2 GenomicFeatures_1.20.1
[3] AnnotationDbi_1.30.1 Biobase_2.28.0
[5] VariantAnnotation_1.14.2 Rsamtools_1.20.4
[7] Biostrings_2.36.1 XVector_0.8.0
[9] GenomicRanges_1.20.5 GenomeInfoDb_1.4.0
[11] IRanges_2.2.4 S4Vectors_0.6.0
[13] BiocGenerics_0.14.0 vimcom_1.2-3
[15] setwidth_1.0-3 colorout_1.1-0
loaded via a namespace (and not attached):
[1] zlibbioc_1.14.0 GenomicAlignments_1.4.1 BiocParallel_1.2.2
BSgenome_1.36.0
[5] tools_3.2.0 DBI_0.3.1 lambda.r_1.1.7
futile.logger_1.4.1
[9] rtracklayer_1.28.4 futile.options_1.0.0 bitops_1.0-6
RCurl_1.95-4.6
[13] biomaRt_2.24.0 RSQLite_1.0.0 XML_3.98-1.2
On 06/11/2015 01:55 AM, Valerie Obenchain wrote:
Thanks for the report.
Now fixed in release (1.14.2) and devel (1.3.25).
Valerie
On 06/09/2015 09:44 AM, Robert Castelo wrote:
hi,
currently, the annotation of variants in intronic regions by
VariantAnnotation and the locateVariants() function does not assign
strand to annotations in introns:
library(VariantAnnotation)
example(locateVariants)
loc_all[loc_all$LOCATION == "intron"]
GRanges object with 2 ranges and 9 metadata columns:
seqnames ranges strand | LOCATION LOCSTART LOCEND
QUERYID TXID CDSID GENEID
<Rle> <IRanges> <Rle> | <factor> <integer> <integer>
<integer> <character> <IntegerList> <character>
chr1 [13302, 13302] * | intron 948 948
3 2 100287102
chr1 [13327, 13327] * | intron 973 973
4 2 100287102
PRECEDEID FOLLOWID
<CharacterList> <CharacterList>
-------
seqinfo: 1 sequence from hg19 genome; no seqlengths
however, introns are stranded, so I would suggest to include the strand
information in variants annotated to intronic regions. After a quick
look to the source code I believe the relevant line is within the
private function .makeResult(), concretely at:
strand=strand(query)[xHits],
where is taking the strand of the query (the variant) while I guess it
should be the subject (the annotation).
cheers,
robert.
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