plot_theta

Character string specifying the directory AND name of the .rlmm file created by <code>Classify</code> (optional)

genotypefile

Character string specifying the directory AND name of the .rlmm file created by <code>Create_Thetafile</code> (optional)

thetafile

At this point, it should always be left as the default FALSE, ie: it is for development purposes only (optional)

Pick.Obj

The name where to store the plot as a .ps file, if blank such as "", it will display on screen instead (optional)

plotfile

A list of SNPs to plot, with one SNP following another on a newline (optional)

snpsfile


 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.


hplot

A classification algorithm, based on a multi-chip, multi-SNP
approach for Affymetrix SNP arrays. Using a large training sample where the
genotype labels are known, this aglorithm will obtain more accurate
classification results on new data. RLMM is based on a robust, linear model
and uses the Mahalanobis distance for classification. The chip-to-chip
non-biological variation is removed through normalization. This model-based
algorithm captures the similarities across genotype groups and probes, as
well as thousands other SNPs for accurate classification.
NOTE: 100K-Xba only at for now.

Nusrat Rabbee

RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

plot_theta function

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.

plot_theta: Allele Summary Plot

Description

Usage

Arguments