removeRedundant

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.

Genotyping assays for bi-allelic markers (e.g. SNPs) produce
signal intensities for the two alleles. 'fitPoly' assigns genotypes
(allele dosages) to a collection of polyploid samples based on these
signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was
limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any
ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011)
<doi:10.1186/1471-2105-12-172>.
New functions added on conversion of data from SNP array software formats,
drawing of XY-scatterplots with or without genotype colors,
checking against expected F1 segregation patterns,
comparing results from two different assays (probes) for the same SNP,
recovery from a saveMarkerModels() crash.

Giorgio Tumino

fitPoly

Genotype Calling for Bi-Allelic Marker Assays

Gerrit Gort

Alejandro Therese Navarro

removeRedundant function

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

Arguments

Remove redundant single-probe markers — removeRedundant

<dl>

<dt>compstat</dt>
<dd>a data.frame as returned by compareProbes in the
compstat item of the return value and in the compfile</dd>


<dt>combscores</dt>
<dd>a data.frame as returned by compareProbes in the</dd>


<dt>compfile</dt>
<dd>a filename to which the compstat part of the results is
written; if NA no file is written</dd>


<dt>combscorefile</dt>
<dd>a filename to which the compscores part of the results is
written; if NA no file is written</dd>

</dl>

removeRedundant: Remove redundant single-probe markers

Description

Usage

Value

Arguments