titv: Classifies SNPs into transitions and transversions

Description Usage Arguments Value See Also Examples

View source: R/titv.R

Description

takes output generated by read.maf and classifies Single Nucleotide Variants into Transitions and Transversions.

Usage

1
titv(maf, useSyn = FALSE, plot = TRUE, file = NULL)

Arguments

maf

an MAF object generated by read.maf

useSyn

Logical. Whether to include synonymous variants in analysis. Defaults to FALSE.

plot

plots a titv fractions. default TRUE.

file

basename for output file name. If given writes summaries to output file. Default NULL.

Value

list of data.frames with Transitions and Transversions summary.

See Also

plotTiTv

Examples

1
2
3
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.titv = titv(maf = laml, useSyn = TRUE)

maftools documentation built on Feb. 6, 2021, 2 a.m.