allele-methods {SeqVarTools} | R Documentation |
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 |
n |
An integer indicating which alternate allele to return. |
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 n
th alternate
allele is returned.
nAlleles
returns an integer vector of the number of alleles
(reference and alternate) for each variant.
Stephanie Gogarten
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)