chr.arm.cnv: Chromosome arm mean CNV

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Obtains a matrix with the weighted average CN per chromosome arm

Usage

chr.arm.cnv(cnv, genome.v = "hg19", verbose = FALSE)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
genome.v	(character) (hg19 or hg38) reference genome version to draw chromosome limits and centromeres
verbose	(logical) whether to return internal messages

Value

a matrix of chromosome arms (rows) versus samples (cols) with average segment logRs per cell

Examples

# initialize CNV data
cnv <- validate.cnv(segdat_lung_ccle)

arm_mat <- chr.arm.cnv(cnv, genome.v="hg19")
dim(arm_mat)

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.