Generate Summary Copy-Number Aberrations Plot

This function was copied and modified from another package (CGHbase). The original code can be found here on github: https://github.com/tgac-vumc/CGHbase The bioconductor page: https://bioconductor.org/packages/release/bioc/html/CGHbase.html

This function creates a summary plot of the copy-number changes of the samples in the provided QDNAseq object.

Usage

SummaryCNPlot(
  x,
  main = "Relative Copy-Number Summary Plot",
  summarytype = "probability",
  maskprob = 0.2,
  maskaberr = 0.1,
  gaincol = "blue",
  losscol = "red",
  misscol = NA,
  build = "GRCh37",
  plotXY = TRUE,
  ...
)

Arguments

x

An S4 object of type QDNAseqCopyNumbers containing multiple samples.

main

(optional) String. Plot Title.

summarytype

(optional) String. One of either 'probability' or 'frequency'.
'probability' - The vertical bars represent the average probability that the positions along the chromosome they cover are gained (blue bars) or lost (red bars) across all samples.
'frequency' - The vertical bars represent the frequency that the positions along the chromosome they cover are gained (blue bars) or lost (red bars) across all samples.

maskprob

(optional) Numeric. Gain or loss probabilities that fall below this number are masked. Used to exclude noise.

maskaberr

(optional) Numeric. Copy-Number gains or losses that fall below this number are masked. Used to exclude noise.