plotCBSsegments: Plots segmented copy number data.

In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description

Plots segmented copy number data.

Usage

plotCBSsegments(
  cbsFile = NULL,
  maf = NULL,
  tsb = NULL,
  savePlot = FALSE,
  ylims = NULL,
  seg_size = 0.1,
  width = 6,
  height = 3,
  genes = NULL,
  ref.build = "hg19",
  writeTable = FALSE,
  removeXY = FALSE,
  color = NULL
)

Arguments

cbsFile	CBS segmented copy number file. Column names should be Sample, Chromosome, Start, End, Num_Probes and Segment_Mean (log2 scale).
maf	optional MAF
tsb	If segmentation file contains many samples (as in gistic input), specify sample name here. Defualt plots all samples. If you are maping maf, make sure sample names in Sample column of segmentation file matches to those Tumor_Sample_Barcodes in MAF.
savePlot	If true plot is saved as pdf.
ylims	Default NULL
seg_size	Default 0.1
width	width of plot
height	height of plot
genes	If given and maf object is specified, maps all mutataions from maf onto segments. Default NULL
ref.build	Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19.
writeTable	If true and if maf object is specified, writes plot data with each variant and its corresponding copynumber to an output file.
removeXY	don not plot sex chromosomes.
color	Manually specify color scheme for chromosomes. Default NULL. i.e, aletrnating Gray70 and midnightblue

Details

this function takes segmented copy number data and plots it. If MAF object is specified, all mutations are highlighted on the plot.

Value

Draws plot

Examples

tcga.ab.009.seg <- system.file("extdata", "TCGA.AB.3009.hg19.seg.txt", package = "maftools")
plotCBSsegments(cbsFile = tcga.ab.009.seg)

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.