PlotMerged: To Make Plots with Merged Regions

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

Description

optional function to make all the regions in 3 fixed log levels (deletion, normal, duplication) and then to plot the samples

Usage

PlotMerged(object, cutoff = 0.1, markers = 20, ...)

Arguments

object	Data object, as returned by ReadData.
cutoff	This cutt of will affect these plots, default is cutoff = 0.1
markers	minimum number of marker required in the region, default is (markers = 20)
...	Sent to plotRegions.

Examples

# 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) 

# Optional function to plot all the amplifications and delections in the same level
PlotMerged(object,comment = TRUE, cutoff = 0.2, markers = 5)

CopyNumber450kCancer documentation built on April 14, 2017, 3:47 p.m.