variantInfo: Variant info
In SeqVarTools: Tools for variant data

Description Usage Arguments Details Value Author(s) See Also Examples

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 `SeqVarGDSClass` object with VCF data.
`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

SeqVarGDSClass

gds <- seqOpen(seqExampleFileName("gds"))
seqSetFilter(gds, variant.sel=1323:1327)
variantInfo(gds, alleles=TRUE)
variantInfo(gds, alleles=TRUE, expanded=TRUE)
expandedVariantIndex(gds)
seqClose(gds)