combine.table: Combine Table
In SeqKat: Detection of Kataegis

Description Usage Arguments Author(s) Examples

View source: R/combine.table.R

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

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

`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.

Fouad Yousif

Fan Fan

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()
	);