test.kataegis: Test Kataegis

In uclahs-cds/public-R-SeqKat: Detection of Kataegis

Test Kataegis

Description

Performs exact binomial test to test the deviation of the 32 tri-nucleotides counts from expected

Usage

test.kataegis(chromosome.num, somatic, units, exprobntcx, output.name, ref.dir,
  chromosome.length.file)

Arguments

chromosome.num	Chromosome
somatic	Data frame of somatic variants
units	Base window size
exprobntcx	Expected probability for each trinucleotide and total number of tcx
output.name	Name of the generated output directory.
ref.dir	Path to a directory containing the reference genome.
chromosome.length.file	A tab separated file containing the lengths of all chromosomes in the reference genome.

Author(s)

Fouad Yousif

Examples

load(
	paste0(
		path.package("SeqKat"),
		"/extdata/test/somatic.rda"
		)
	);

load(
	paste0(
		path.package("SeqKat"),
		"/extdata/test/exprobntcx.rda"
		)
	);

example.chromosome.length.file <- paste0(
	path.package("SeqKat"),
	"/extdata/test/length_hg19_chr_test.txt"
	);

example.ref.dir <- paste0(
	path.package("SeqKat"),
	"/extdata/test/ref/"
	);

test.kataegis(
	4,
	somatic,
	2,
	exprobntcx,
	tempdir(),
	example.ref.dir,
	example.chromosome.length.file
	);

uclahs-cds/public-R-SeqKat documentation built on May 31, 2024, 9:10 p.m.