isSNV {SeqVarTools} | R Documentation |
Flag single nucleotide variants
## S4 method for signature 'SeqVarGDSClass' isSNV(gdsobj, biallelic=TRUE)
gdsobj |
A |
biallelic |
A logical indicating whether only biallelic SNVs are considered. |
If biallelic=TRUE
, a variant is considered a single nucleotide variant (SNV) if there is
one reference allele and one alternate allele, each one base in
length. If biallelic=FALSE
, there may be multiple alternate
alleles, each one base in length.
Setting biallelic=TRUE
is considerably faster for large data sets.
A logical vector indicating which variants are SNVs.
Stephanie Gogarten
SeqVarGDSClass
,
allele-methods
,
applyMethod
gds <- seqOpen(seqExampleFileName("gds")) table(isSNV(gds)) seqClose(gds)