getRS-methods: method that convert segment data into reduced segment matrix

In CNTools: Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Description

getRS takes a CNSeg object containing the output of the segment function of DNAcopy and format the data into a matrix based on overlapping chromosome region (by = region", gene (by = gene) or pair overlapping chromosome region (by = pair)

Methods

object = "CNSeg"

a reduced segment can be generated in three ways; by chromosomal regions that overlap across sample (by = region), by genes (by = gene), or by pair of samples with chromosome regions aligned (by = pair). User may choose to imput cells (by region or gene only) where a value can not be assigned by setting imput = TRUE. The X and Y chromosomes can dropped by stting XY = FALSE.

CNTools documentation built on Nov. 8, 2020, 8:21 p.m.