plot LRR, BAF, and the copy number estimates

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Description

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

Usage

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

Arguments

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

Author(s)

Wei Sun

See Also

genoCNA, genoCNV

Examples

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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")