create_Thetafile: Calculating Parameter Estimates

In RLMM: A Genotype Calling Algorithm for Affymetrix SNP Arrays

Description

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.

Usage

create_Thetafile(probefiledir = getwd(),
                 start = 1,
                 end = -1,
                 thetafile = "")

Arguments

probefiledir	Character string specifying the directory with the *.norm files (optional)
start	An integer value specifying which SNP number we should start at when calculating the theta values (optional)
end	An integer value specifying which SNP number we should stop at when calculating the theta values (optional)
thetafile	A character string specifying the name the theta file will be saved as (optional)

Author(s)

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

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