plotCBSsegments: Plots segmented copy number data.

Description Usage Arguments Details Value Examples

View source: R/plot_cbs_segs.R

Description

Plots segmented copy number data.

Usage

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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 head 1 sample. Set 'ALL' for plotting 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

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

maftools documentation built on Feb. 6, 2021, 2 a.m.