getRearrClass: CNomplexity::getRearrClass

In SteeleCD/CNomplexity: Analysis of Complex Copy Cumber and Structural Variants in Cancer Genomes.

Description

Categorise rearrangements into classes for input into non-negative matrix factorisation. Categorised by rearrangement type, rearrangement size, and un/clu stered status.

Usage

getRearrClass(sample,chrom1,start1,end1,
	chrom2,start2,end2,type) 

Arguments

sample	String vector. Sample for each rearrangement.
chrom1	String vector. First partner chromosome for each rearrangement.
start1	String vector. First partner start position for each rearrangement.
end1	String vector. First partner end position for each rearrangement.
chrom2	String vector. Second partner chromosome for each rearrangement.
start2	String vector. Second partner start position for each rearrangement.
end2	String vector. Second partner end position for each rearrangement.
type	String vector. Structural variant type for each rearrangement e.g. deletion, inversion, tandem-duplication or translocation.

Details

Rearrangement classes are described in Nik-Zainal et al. (2016).

Value

Vector of rearrangement classes.

SteeleCD/CNomplexity documentation built on May 29, 2019, 2:09 p.m.