plotRegions: Genomic Copy Number Plotting Function

In Molmed/CopyNumber450kCancer: Baseline Correction for Copy Number Data from Cancer Samples

Description

To be used internally by the package only.

This function plots the chromosomal regions (segments) with colored segments based on the cutoff. This function was built based on "plotSample" function in "CopyNumber450k" package (http://www.bioconductor.org/packages/release/bioc/html/CopyNumber450k.html), and uses a modified "minor.tick" function in "Hmisc" package to draw small tick in the plots.

Usage

plotRegions(object, chr, start, end, cutoff = 0.1, markers = 20, ...)

Arguments

object	Data object, as returned by ReadData.
chr	Chromosomes to plot.
start	Start positions of region to plot.
end	End position of region to plot.
cutoff	Log R ratio cutoff.
markers	Minimum number of markers per segment cutoff. Less than this number the segment will not be plotted.
...	Sent to plot.

Examples

#To be used internally by the package only

# the package contains example files: regions.csv and sample_list.csv
#to load the example regions.csv and sample_list.csv files
regions <- system.file("extdata", "regions.csv", package="CopyNumber450kCancer")
sample_list <- system.file("extdata", "sample_list.csv", package="CopyNumber450kCancer")

# Creat the object for the package
object <- ReadData(regions,sample_list) 

#to plot all the regions and all the sampls in one plot
plotRegions(object$regions)

Molmed/CopyNumber450kCancer documentation built on Sept. 2, 2020, 8:23 a.m.