`expand()` and non-standard rowRanges columns

Reproduisez l’exemple R fourni avec VariantAnnotation et comparez rowRanges(vcf) avant et après expand(vcf). Commencez par localiser l’implémentation de expand() pour CollapsedVCF ; le travail est terminé lorsque l’objet développé conserve les colonnes non standard de rowRanges, telles que SNP_name et num_alts, pour chaque ligne obtenue.

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