final.score {SeqKat}

Final Score

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()
	);