pseudoautoIntensityPlot: Plot B Allele Frequency and Log R Ratio for the X and Y...
In amstilp/GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Author(s) References See Also Examples

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

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

`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`.

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.

Caitlin McHugh

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.

pseudoautosomal, IntensityData, GenotypeData, BAFfromGenotypes

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)