selMarkers_qall

In order to get an idea of the quality of markers with
different levels of qall, this function samples marker numbers at a
specified set of qall values.

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_qall function

<dl><dt>chk</dt>
<dd>a data frame as returned by checkF1</dd>
<dt>qall_levels</dt>
<dd>a numeric vector with the levels of the quality
parameter (qall_mult or qall_weights, see parameter qall_flavo)
at which markers should be selected</dd>
<dt>mrkperlevel</dt>
<dd>the number of markers to select per level of qall</dd>
<dt>qall_flavor</dt>
<dd>which qall to use: by default qall_mult,
also qall_weights is possible</dd></dl>

Arguments

Sample markers at several qall levels — selMarkers_qall

<dl>

<dt>chk</dt>
<dd>a data frame as returned by checkF1</dd>


<dt>qall_levels</dt>
<dd>a numeric vector with the levels of the quality
parameter (qall_mult or qall_weights, see parameter qall_flavo)
at which markers should be selected</dd>


<dt>mrkperlevel</dt>
<dd>the number of markers to select per level of qall</dd>


<dt>qall_flavor</dt>
<dd>which qall to use: by default qall_mult,
also qall_weights is possible</dd>

</dl>

selMarkers_qall: Sample markers at several qall levels

Description

Usage

Value

Arguments