SeqKat (version 0.0.9)

get.exprobntcx: get.exprobntcx

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

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)