combine.table {SeqKat}

Combine Table

Description

Merges overlapped windows to identify genomic boundaries of kataegic events. This function also assigns hypermuation and kataegic score for combined windows

Usage

combine.table(test.table, somatic, mutdistance, segnum, output.name)

Arguments

test.table

Data frame of kataegis test scores

somatic

Data frame of somatic variants

mutdistance

The maximum intermutational distance allowed for SNVs to be grouped in the same kataegic event. Recommended value: 3.2

segnum

Minimum mutation count. The minimum number of mutations required within a cluster to be identified as kataegic. Recommended value: 4

output.name

Name of the generated output directory.

Author(s)

Fouad Yousif

Fan Fan

Examples

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

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

combine.table(
	final.score,
	somatic,
	3.2,
	4,
	tempdir()
	);