create_Thetafile

Character string specifying the directory with the *.norm files (optional)

probefiledir

An integer value specifying which SNP number we should start at when calculating the theta values (optional)

start

An integer value specifying which SNP number we should stop at when calculating the theta values (optional)

A character string specifying the name the theta file will be saved as (optional)

thetafile


Assuming that the *.norm files are created, this step of the data analysis will calculate estimates of theta A and theta B values for each SNP and chip based on normalized probe intensity data from the *.norm files. The theta values are produced from fitting a probe-level additive model to the log2 A probe
intensities and the B intensities separately.


methods

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

create_Thetafile function

Assuming that the *.norm files are created, this step of the data analysis will calculate estimates of theta A and theta B values for each SNP and chip based on normalized probe intensity data from the *.norm files. The theta values are produced from fitting a probe-level additive model to the log2 A probe
intensities and the B intensities separately.

create_Thetafile: Calculating Parameter Estimates

Description

Usage

Arguments