allele-methods: Extract allele information from a GDS object
In SeqVarTools: Tools for variant data

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

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

## S4 method for signature 'SeqVarGDSClass'
refChar(gdsobj)
## S4 method for signature 'SeqVarGDSClass'
altChar(gdsobj, n=0)
## S4 method for signature 'SeqVarGDSClass'
nAlleles(gdsobj)

`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.

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

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.

Stephanie Gogarten

SeqVarGDSClass, applyMethod

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)