plotAllCNVs: plotAllCNVs

In CNVfilteR: Identifies false positives of CNV calling tools by using SNV calls

Description

Plots all CNVs on chromosome ideograms

Usage

plotAllCNVs(cnvs.gr, genome = "hg19")

Arguments

cnvs.gr	GRanges containing al CNV definitions returned by filterCNVs or loadCNVcalls functions.
genome	The name of the genome. (Defaults to "hg19")

Details

Plots all CNVs defined at cnvs.gr on a view of horizontal ideograms representing all chromosomes.

Value

invisibly returns a karyoplot object

Examples

cnvs.file <- system.file("extdata", "DECoN.CNVcalls.2.csv", package = "CNVfilteR", mustWork = TRUE)
cnvs.gr <- loadCNVcalls(cnvs.file = cnvs.file, chr.column = "Chromosome", start.column = "Start", end.column = "End", cnv.column = "CNV.type", sample.column = "Sample")

# Plot all CNVs
plotAllCNVs(cnvs.gr)

CNVfilteR documentation built on April 17, 2021, 6:06 p.m.