Plot B Allele Frequency and Log R Ratio for the X and Y chromosomes, overlaying XY SNPs

Description

This function plots X, Y and pseudoautosomal SNPs on BAF/LRR plots.

Usage

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pseudoautoIntensityPlot(intenData, scan.ids, main=NULL,
  plotY=FALSE, hg.build=c("hg18", "hg19"),
  snp.exclude = NULL, cex=0.5, ...)

Arguments

scan.ids

A vector containing the sample indices of the plots.

intenData

IntensityData object, must contain 'BAlleleFreq' and 'LogRRatio'

main

A character vector containing the titles to be used for each plot. If NULL then the title will be the sample number and the chromosome.

plotY

If plotY is TRUE, the Y chromosome will be plotted in addition to X.

hg.build

Human genome bulid number

snp.exclude

An integer vector giving the IDs of SNPs to exclude from the plot.

cex

cex value for points on the plots

...

Other parameters to be passed directly to plot.

Details

The pseudoautosomal regions are highlighted on the plots (PAR1 and PAR2 in gray, XTR in yellow), and the X, Y, and XY SNPs are plotted in different colors. The base positions for these regions depend on genome build (hg.build). Currently hg18 and hg19 are supported.

By default the output is a 2-panel plot with LRR and BAF for the X chromosome. if plotY is TRUE, the output is a 4-panel plot with the Y chromosome plotted as well.

Author(s)

Caitlin McHugh

References

Ross, Mark. T. et al. (2005), The DNA sequence of the human X chromosome. Nature, 434: 325-337. doi:10.1038/nature03440

Mumm, S., Molini, B., Terrell, J., Srivastava, A., and Schlessinger, D. (1997), Evolutionary features of the 4-Mb Xq21.3 XY homology region revealed by a map at 60-kb resolution. Genome Res. 7: 307-314.

See Also

pseudoautosomal, IntensityData, GenotypeData, BAFfromGenotypes

Examples

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library(GWASdata)
data(illuminaScanADF)
blfile <- system.file("extdata", "illumina_bl.gds", package="GWASdata")
blgds <- GdsIntensityReader(blfile)
intenData <-  IntensityData(blgds, scanAnnot=illuminaScanADF)

scanID <- getScanID(illuminaScanADF, index=1)
pseudoautoIntensityPlot(intenData=intenData, scan.ids=scanID)
close(intenData)

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