plotCN {genoCN} | R Documentation |
plot LRR, BAF, and the copy number estimates of genoCNV and/or PennCNV.
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)
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 |
Wei Sun