expand() and non-standard rowRanges columns #85
Description
hi there,
is there a way to retain non-standard rowRanges columns when I use expand() on a CollapsedVCF object? Some demo code below.
If not, please can you consider this an enhancement request? thanks!
all the best,
Janet
library(VariantAnnotation)
vcf <- VCF(rowRanges = GRanges("chr1", IRanges(1:4*3, width=c(1, 2, 1, 1))))
alt(vcf) <- DNAStringSetList("A", c("TT"), c("G", "A"), c("TT", "C"))
ref(vcf) <- DNAStringSet(c("G", c("AA"), "T", "G"))
## add some non-standard columns to rowRanges
mcols(rowRanges(vcf))$SNP_name <- paste("SNP_", 1:length(vcf), sep="")
mcols(rowRanges(vcf))$num_alts <- elementNROWS(alt(vcf))
## take a look
rowRanges(vcf)
GRanges object with 4 ranges and 6 metadata columns:
seqnames ranges strand | SNP_name num_alts REF ALT QUAL
<Rle> <IRanges> <Rle> | <character> <integer> <DNAStringSet> <DNAStringSetList> <numeric>
[1] chr1 3 * | SNP_1 1 G A NA
[2] chr1 6-7 * | SNP_2 1 AA TT NA
[3] chr1 9 * | SNP_3 2 T G,A NA
[4] chr1 12 * | SNP_4 2 G TT,C NA
FILTER
<character>
[1] <NA>
[2] <NA>
[3] <NA>
[4] <NA>
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
## those extra columns are lost when we expand
vcfLong <- expand(vcf)
rowRanges(vcfLong)
rowRanges(vcfLong)
GRanges object with 6 ranges and 4 metadata columns:
seqnames ranges strand | REF ALT QUAL FILTER
<Rle> <IRanges> <Rle> | <DNAStringSet> <DNAStringSet> <numeric> <character>
[1] chr1 3 * | G A NA <NA>
[2] chr1 6-7 * | AA TT NA <NA>
[3] chr1 9 * | T G NA <NA>
[4] chr1 9 * | T A NA <NA>
[5] chr1 12 * | G TT NA <NA>
[6] chr1 12 * | G C NA <NA>
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths