Description Usage Arguments Examples
Uses the regions object, this function will plot the last modified regions object (i.e. after the autocorrection or the reviewing)
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object |
Data object, as returned by |
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 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #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
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