CopyNumber450kCancer (version 1.0.3)

PlotCNV: Plot the CNV Regions with the Density Plot

Description

Uses the regions object, this function will plot the last modified regions object (i.e. after the autocorrection or the reviewing)

Usage

PlotCNV(object, select, comment = F, cutoff = 0.1, markers = 20)

Arguments

object

Data object, as returned by ReadData.

select

The number of the samples to be reviewed, if not determined then all the samples in the sample list will be selected

comment

If TRUE then the comment in the sample list file will be printed in the header of the plots, default is FALSE

cutoff

cutoff for the segments coloring , default is cutoff = 0.1

markers

the minimum number of markers in the segment to be plotted, default is markers = 20

Examples

#example
# 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) 

# Baseline autocorrection, 
# this will creat different plot and QC and new regions file in the working directory
object <- AutoCorrectPeak(object)

# For manual revision and manual baseline determination
# object <- ReviewPlot(object)

# To plot the final plots
PlotCNV(object) # to plot all the samples
PlotCNV(object, select= c(1,4), comment=FALSE, cutoff=0.1, markers=20) # to plot some samples