test.kataegis {SeqKat}

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
	);