plotSample: Plot the data and results for a single sample

In mskcc/facets: Cellular Fraction and Copy Numbers from Tumor Sequencing

Description

Plots copy number log-ratio, variant allele log-odds ratio as well as the copy number and cellular fraction fits.

Usage

  plotSample(x, emfit=NULL, clustered=FALSE, plot.type=
                c("em","naive","both","none"), sname=NULL)

Arguments

x	output from procSample
emfit	output of emcncf
clustered	indicator of whether segment or cluster summary plotted
plot.type	the type of plot. The default is em in which the logR and logOR data as well as the copy number and cellular fraction fits from EM are graphed. For naive the naive copy number and cellular fraction fits are used instead of EM. For none only the data are shown and for both both fits are shown.
sname	sample name give as a character string.

mskcc/facets documentation built on Oct. 15, 2021, 3:12 p.m.