selMarkers_byR

Select markers based on their R statistics, for studying
the relation between R level and marker quality

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

selMarkers_byR function

<dl><dt>Rstats</dt>
<dd>a data frame as returned by calcRstats</dd>
<dt>Rlevels</dt>
<dd>a vector of R levels in increasing order (preferably from
the minimum to the maximum of stat over all markers in Rstats)</dd>
<dt>mrkperlevel</dt>
<dd>number, default 1: the number of markers to select at
each of the levels in Rlevels</dd>
<dt>stat</dt>
<dd>the name of one of the statistics columns in Rstats</dd></dl>

Arguments

Select markers at specified R levels — selMarkers_byR

<dl>

<dt>Rstats</dt>
<dd>a data frame as returned by calcRstats</dd>


<dt>Rlevels</dt>
<dd>a vector of R levels in increasing order (preferably from
the minimum to the maximum of stat over all markers in Rstats)</dd>


<dt>mrkperlevel</dt>
<dd>number, default 1: the number of markers to select at
each of the levels in Rlevels</dd>


<dt>stat</dt>
<dd>the name of one of the statistics columns in Rstats</dd>

</dl>

selMarkers_byR: Select markers at specified R levels

Description

Usage

Value

Arguments

Details