R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Plot B Allele Frequency and Log R Ratio for the X and Y...

pseudoautoIntensityPlot

R Documentation

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

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.

Examples

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GWASTools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/pseudoautoIntensityPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pseudoautoIntensityPlot
> ### Title: Plot B Allele Frequency and Log R Ratio for the X and Y
> ###   chromosomes, overlaying XY SNPs
> ### Aliases: pseudoautoIntensityPlot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>