plot_theta: Allele Summary Plot

In RLMM: A Genotype Calling Algorithm for Affymetrix SNP Arrays

Description

Creates an Allele Summary plot (allele B vs. allele A) for each SNP specified in snpsfilename. The points in the plot are the (theta A, theta B) ordered pairs for all the samples of the SNP. If a plotfilename is specified, it will save the plot as a .ps file, otherwise the plot is shown on screen.

Usage

plot_theta(genotypefile = "Xba.rlmm",
	   thetafile = "Xba.theta",
	   Pick.Obj = "FALSE",
	   plotfile = "plots.ps",
	   snpsfile = "snps.lst")

Arguments

genotypefile	Character string specifying the directory AND name of the .rlmm file created by Classify (optional)
thetafile	Character string specifying the directory AND name of the .rlmm file created by Create_Thetafile (optional)
Pick.Obj	At this point, it should always be left as the default FALSE, ie: it is for development purposes only (optional)
plotfile	The name where to store the plot as a .ps file, if blank such as "", it will display on screen instead (optional)
snpsfile	A list of SNPs to plot, with one SNP following another on a newline (optional)

Author(s)

Nusrat Rabbee <[e-mail]>, Gary Wong <[e-mail]>

RLMM documentation built on Nov. 8, 2020, 6:20 p.m.