plot_theta {RLMM}R Documentation

Allele Summary Plot

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 <nrabbee@post.harvard.edu>, Gary Wong <wongg62@gmail.com>


[Package RLMM version 1.4.0 Index]