titv {SeqVarTools} | R Documentation |
Calculate transition/transversion ratio overall or by sample
## S4 method for signature 'SeqVarGDSClass' titv(gdsobj, by.sample=FALSE, use.names=FALSE)
gdsobj |
A |
by.sample |
A logical indicating whether TiTv should be calculated by sample or overall for the entire GDS object. |
use.names |
A logical indicating whether to assign
sample IDs as names of the output vector (if |
If by.sample=FALSE
(the default), titv
calulates the
transition/transversion ratio (TiTv) over all samples.
If by.sample=TRUE
, titv
calculates TiTv over all
variant genotypes (heterozygous or homozygous non-reference) for each
sample.
A single value for TiTv if by.sample=FALSE
. If by.sample=TRUE
,
a numeric vector containing TiTv for each sample.
Stephanie Gogarten
SeqVarGDSClass
,
applyMethod
,
isVariant
gds <- seqOpen(seqExampleFileName("gds")) titv(gds) titv(gds, by.sample=TRUE) ## apply to a subset of variants library(GenomicRanges) chrom <- seqGetData(gds, "chromosome") pos22 <- seqGetData(gds, "position")[chrom == 22] ranges <- GRanges(seqnames="22", IRanges(min(pos22), max(pos22))) applyMethod(gds, titv, ranges) seqClose(gds)