get.exprobntcx: get.exprobntcx

In SeqKat: Detection of Kataegis

Description

Gets the expected probability for each trinucleotide and total number of tcx

Usage

get.exprobntcx(somatic, ref.dir, trinucleotide.count.file)

Arguments

somatic	Data frame of somatic variants
ref.dir	Path to a directory containing the reference genome.
trinucleotide.count.file	A tab seprarated file containing a count of all trinucleotides present in the reference genome. This can be generated with the get.trinucleotide.counts() function in this package.

Author(s)

Fan Fan

Fouad Yousif

Examples

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

trinucleotide.count.file <- paste0(
	path.package("SeqKat"),
	"/extdata/tn_count.txt"
	);

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

get.exprobntcx(somatic, example.ref.dir, trinucleotide.count.file)

SeqKat documentation built on March 13, 2020, 1:59 a.m.