plotCN {genoCN} | R Documentation |
plot LRR, BAF, and the copy number estimates of genoCNV and/or PennCNV.
plotCN(pos, LRR, BAF, chr2plot = NULL, sampleIDs = NULL, fileNames=NULL, types = "genoCN", CNA = TRUE, main = "", LRR.ylim=NULL, cex=0.5, plot.lowess=TRUE)
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 chromosome to plot. Only one chromosome 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. |
fileNames |
one or more names of the output files of genoCN or PennCNV. If it is NULL, only plot the LRR and BAF. |
types |
should be the same length as fileNames, indicating the type of output, currently 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
data(snpData) data(snpInfo) dim(snpData) dim(snpInfo) snpData[1:2,] snpInfo[1:2,] snpInfo[c(1001,1100,10001,10200),] plotCN(pos=snpInfo$Position, LRR=snpData$LRR, BAF=snpData$BAF, main = "simulated data on Chr22")