R: Plot signal and breakpoints with segment-level signal...

plotSeg

R Documentation

Plot signal and breakpoints with segment-level signal estimates

Description

Plot signal and breakpoints with segment-level signal estimates

Usage

plotSeg(dat, breakpoints = NULL, regNames = NULL,
  exclNames = c("genotype", "region", "bT", "bN", "cellularity"),
  ylabs = colnames(dat), ylims = NULL, binExclPattern = "^b[N|T]*$",
  col = "#33333333", pch = 19, cex = 0.3)

Arguments

`dat`	A `matrix` or data frame whose rows correspond to loci sorted along the genome, or a `numeric` `vector`.
`breakpoints`	A vector of breakpoints positions, or a `list` of such vectors.
`regNames`	Region labels, a vector of length `length(breakpoints)+1` (if `breakpoints` is a vector) or of length `length(breakpoints[[1]])+1` (if `breakpoints` is a list).
`exclNames`	A vector of column names corresponding to columns that should not be plotted.
`ylabs`	A vector of 'y' labels (column names or indices) that should be plotted.
`ylims`	An optional 2d* matrix with `ylim` values for each of the d dimensions to be plotted.
`binExclPattern`	A vector of column names or indices in `colnames(dat)` for which segment-level signal estimates should not be drawn.
`col`	Color of plotting symbol, see `par`
`pch`	Plotting symbol, see `par`
`cex`	Magnification factor for plotting symbol, see `par`

Details

Argument 'binCols' is mainly used to avoid calculating mean levels for allelic ratios, which would not make sense as they are typically multimodal.

Author(s)

Morgane Pierre-Jean and Pierre Neuvial

Examples


affyDat <- acnr::loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
sim <- getCopyNumberDataByResampling(1e4, 5, minLength=100, regData=affyDat)
dat <- sim$profile
res <- PSSeg(dat, method="RBS", stat=c("c", "d"), K=50)
bkpList <- list(true=sim$bkp, est=res$bestSeg)
plotSeg(dat, breakpoints=bkpList)