SeqVarTools (version 1.10.0)

allele-methods: Extract allele information from a GDS object

Description

Extract reference and alternate alleles and allele counts from a GDS object.

Usage

"refChar"(gdsobj)
"altChar"(gdsobj, n=0)
"nAlleles"(gdsobj)

Arguments

gdsobj

A SeqVarGDSClass object with VCF data.

n

An integer indicating which alternate allele to return. n=0 returns a comma-separated string of all alternate alleles.

Value

refChar returns a character vector of reference alleles.altChar returns a character vector of alternate alleles. If n=0, multiple alternate alleles are represented as a comma-separated string. If n>0, only the nth alternate allele is returned.nAlleles returns an integer vector of the number of alleles (reference and alternate) for each variant.

Details

These methods parse the "allele" field of a GDS object.

See Also

SeqVarGDSClass, applyMethod

Examples

gds <- seqOpen(seqExampleFileName("gds"))
table(refChar(gds))
table(altChar(gds))
table(altChar(gds, n=1))
table(altChar(gds, n=2), useNA="ifany")
table(nAlleles(gds))
seqClose(gds)