calcRstats

Calculate the min, max, mean and 50
for each marker

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

calcRstats function

<dl><dt>datpoly</dt>
<dd>a data frame in long format (input format for fitPoly)
with at least columns MarkerName, SampleName, R</dd>
<dt>out</dt>
<dd>name of output file; if NA no file is written. File contains
the same data as the return value</dd></dl>

Arguments

Calculate statistics of R per marker — calcRstats

<dl>

<dt>datpoly</dt>
<dd>a data frame in long format (input format for fitPoly)
with at least columns MarkerName, SampleName, R</dd>


<dt>out</dt>
<dd>name of output file; if NA no file is written. File contains
the same data as the return value</dd>

</dl>

calcRstats: Calculate statistics of R per marker

Description

Usage

Value

Arguments

Details