final.score: Final Score

In SeqKat: Detection of Kataegis

Description

Assigns hypermutation score (hm.score) and kataegic score (k.score)

Usage

final.score(test.table, cutoff, somatic, output.name)

Arguments

test.table	Data frame of kataegis test scores
cutoff	The minimum hypermutation score used to classify the windows in the sliding binomial test as significant windows. The score is calculated per window as follows: -log10(binomial test p-value). Recommended value: 5
somatic	Data frame of somatic variants
output.name	Name of the generated output directory.

Author(s)

Fan Fan

Fouad Yousif

Examples

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

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

final.score(
	test.table,
	5,
	somatic,
	tempdir()
	);

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