titv: Classifies SNPs into transitions and transversions

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Classifies SNPs into transitions and transversions

Description

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

Usage

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

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

PoisonAlien/maftools documentation built on Sept. 15, 2024, 10:06 a.m.