plotCN {genoCN}R Documentation

plot LRR, BAF, and the copy number estimates

Description

plot LRR, BAF, and the copy number estimates of genoCNV and/or PennCNV.

Usage

plotCN(fileNames, pos, LRR = NULL, BAF = NULL, chr2plot = NULL, 
sampleIDs = NULL, types = "genoCN", CNA = TRUE, main = "", LRR.ylim=NULL,
cex=0.5, plot.lowess=TRUE)

Arguments

fileNames one or more names of the output files of genoCNV or PennCNV
pos position of all the SNPs
LRR a vector of the log R ratio, should be one-to-one correspondence of pos
BAF a vector of the B allele frequency, should be one-to-one correspondence of pos
chr2plot which chromsome to plot. Only one chromsome can be plotted each time
sampleIDs sample ID, could be a vector of the same length as fileNames so that different sample IDs are used for different input files.
types should be the same length as fileNames, indicating the type of output, currently only only support "genoCN" and "pennCNV"
CNA whether this is a copy number aberration study.
main title of the plot
LRR.ylim Range of y-axis for LRR plot
cex the amount by which plotting text and symbols should be magnified relative to the default
plot.lowess to plot the lowess curve for LRR or not

Author(s)

Wei Sun

See Also

genoCNA, genoCNV


[Package genoCN version 1.06 Index]