removeRedundant: Remove redundant single-probe markers

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Remove redundant single-probe markers

Description

If for a SNP both probes produced very similar results, function compareProbes generated an extra marker combining the results from both probes. In that case the original single-probe markers are redundant and this function removes those data from the compstat and combscores data frames.

Usage

removeRedundant(compstat, combscores, compfile, combscorefile)

Arguments

compstat	a data.frame as returned by compareProbes in the compstat item of the return value and in the compfile
combscores	a data.frame as returned by compareProbes in the
compfile	a filename to which the compstat part of the results is written; if NA no file is written
combscorefile	a filename to which the compscores part of the results is written; if NA no file is written

Value

A list with two components, compstat and combscores. These are identical to the parameters compstat and combscores, with the redundant single-probe markers removed.For their contents see function compareProbes.

fitPoly documentation built on April 3, 2025, 8:58 p.m.