plotCN: plot LRR, BAF, and the copy number estimates

In genoCN: genotyping and copy number study tools

Description

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

Usage

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

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")

Example output

[1] 17348     3
[1] 17348     4
       Name        LRR         BAF
1 rs2334386 -0.2440655 1.000000000
2 rs9617528 -0.1422038 0.007824231
             Name Chr Position   PFB
1075853 rs2334386  22 14430353 0.956
1075854 rs9617528  22 14441016 0.176
              Name Chr Position   PFB
1076853  rs1934895  22 17460150 0.140
1076952  rs1206549  22 17595860 0.740
1085853 rs17750152  22 35827972 0.856
1086052  rs8141057  22 36007895 0.780

genoCN documentation built on Nov. 8, 2020, 8:12 p.m.