Hi,
I discovered the following problem in the geno() elements of the VCF object
when I load multiple regions from a .vcf file:
## Correct
> tmp = readVcf(system.file("extdata", "chr22.vcf.gz",
> package="VariantAnnotation"), "hg19")[1:10]
> geno(tmp)$GT
HG00096 HG00097 HG00099 HG00100 HG00101
rs7410291 "0|0" "0|0" "1|0" "0|0" "0|0"
rs147922003 "0|0" "0|0" "0|0" "0|0" "0|0"
rs114143073 "0|0" "0|0" "0|0" "0|0" "0|0"
rs141778433 "0|0" "0|0" "0|0" "0|0" "0|0"
rs182170314 "0|0" "0|0" "0|0" "0|0" "0|0"
rs115145310 "0|0" "0|0" "0|0" "0|0" "0|0"
rs186769856 "0|0" "0|0" "0|0" "0|0" "0|0"
rs77627744 "0|0" "0|0" "0|0" "0|0" "0|0"
rs193230365 "0|0" "0|0" "0|0" "0|0" "0|0"
rs9627788 "0|0" "0|0" "1|0" "0|0" "0|0"
## Wrong: Load regions separately using ScanVcfParam(which= )
> tmp2 = readVcf(system.file("extdata", "chr22.vcf.gz",
> package="VariantAnnotation"), "hg19", param=ScanVcfParam(which=rowData(tmp)))
> geno(tmp2)$GT
HG00096 HG00097 HG00099 HG00100 HG00101
rs7410291 "0|0" "0|0" "0|0" "0|0" "0|0"
rs147922003 "0|0" "0|0" "0|0" "0|0" "0|0"
rs114143073 "1|0" "0|0" "0|0" "0|0" "0|0"
rs141778433 "0|0" "0|0" "0|0" "0|0" "0|0"
rs182170314 "0|0" "0|0" "0|0" "0|0" "0|0"
rs115145310 "0|0" "0|0" "0|0" "0|0" "0|0"
rs186769856 "0|0" "0|0" "0|0" "0|0" "0|0"
rs77627744 "0|0" "0|0" "0|0" "0|0" "1|0"
rs193230365 "0|0" "0|0" "0|0" "0|0" "0|0"
rs9627788 "0|0" "0|0" "0|0" "0|0" "0|0"
Note how the elements have been added by column instead of by row.
The following solved the issue for me:
$svn diff VariantAnnotation/
Index: VariantAnnotation/R/AllUtilities.R
===================================================================
--- VariantAnnotation/R/AllUtilities.R (revision 73920)
+++ VariantAnnotation/R/AllUtilities.R (working copy)
@@ -62,8 +62,8 @@
cmb
} else {
trans <- lapply(elt, t)
- cmb <- matrix(t(do.call(c, trans)),
- length(lst[["rowData"]]), d[2])
+ cmb <- matrix(do.call(c, trans),
+ length(lst[["rowData"]]), d[2], byrow=TRUE)
cmb
}
})
My suspicion is that the transposition t() on line 65 didn't do the desired
job, as do.call() returned a vector..
I don't fully understand the code, so it may be worth double checking.
For example, I didn't check the case when the individual geno entries contain
more than a single value for each variant and sample.
The same problem also occurred for VariantAnnotation_1.4.9.
Best wishes,
Moritz
P.S.
> sessionInfo()
R Under development (unstable) (2013-02-05 r61843)
Platform: x86_64-apple-darwin11.4.2 (64-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] VariantAnnotation_1.5.41 Rsamtools_1.11.20 Biostrings_2.27.11
[4] biomaRt_2.15.0 GenomicRanges_1.11.34 IRanges_1.17.35
[7] BiocGenerics_0.5.6 BiocInstaller_1.9.6 RColorBrewer_1.0-5
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.21.12 Biobase_2.19.2 bitops_1.0-5
[4] BSgenome_1.27.1 DBI_0.2-5 GenomicFeatures_1.11.13
[7] RCurl_1.95-3 RSQLite_0.11.2 rtracklayer_1.19.9
[10] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1
[13] zlibbioc_1.5.0
---
Moritz Gerstung
Postdoctoral Fellow
Cancer Genome Project
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SA
UK
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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