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titv

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

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)
maftools

Summarize, Analyze and Visualize MAF Files

v2.6.05
MIT + file LICENSE
Authors
Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)
Initial release
2015-12-14

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