plotSample: Plot the data and results for a single sample

In rptashkin/facets2n: Cellular Faction and Copy Numbers from Tumor Sequencing

Plot the data and results for a single sample

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	(character) output from procSample
emfit	(character) output of emcncf
clustered	(logical) indicator of whether segment or cluster summary plotted
plot.type	(character) 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	(character) sample name give as a character string

rptashkin/facets2n documentation built on May 11, 2022, 1:34 p.m.