variantInfo {SeqVarTools} | R Documentation |
Return basic variant info as a data.frame.
## S4 method for signature 'SeqVarGDSClass' variantInfo(gdsobj, alleles=TRUE, expanded=FALSE) ## S4 method for signature 'SeqVarGDSClass' expandedVariantIndex(gdsobj)
gdsobj |
A |
alleles |
A logical value for whether to include ref and alt alleles |
expanded |
A logical value for whether to expand multi-allelic variants with one row per alternate allele. |
Variants can be represented in collapsed form, with one row per variant, or in expanded form, with one row per alternate allele for multiallelic variants.
variantInfo
returns a data.frame with variant.id, chromosome, and position for each variant. If alleles=TRUE
, the data.frame includes ref and alt. If expanded=TRUE
, the data.frame includes allele.index, which is 1 for the first alternate allele, 2 for the second alternate, etc.
expandedVariantIndex
returns an index to transform a vector or matrix from collapsed to expanded form.
Stephanie Gogarten
gds <- seqOpen(seqExampleFileName("gds")) seqSetFilter(gds, variant.sel=1323:1327) variantInfo(gds, alleles=TRUE) variantInfo(gds, alleles=TRUE, expanded=TRUE) expandedVariantIndex(gds) seqClose(gds)