saveMarkerModels

This is the old name of the function `fitMarkers()`, the main function
of `fitPoly`. It is kept only for backwards-compatibility. The only difference between
the two is the default parameter of the genotyping probability threshold `p.threshold`, 
it is 0.99 in `saveMarkerModels()` (as was originally set) and it is 0.9 in the current
`fitMarkers()`.

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

saveMarkerModels function

<dl><dt>...</dt>
<dd>All parameters allowed in the function `fitMarkers()`. For a full description
see the help of that function.</dd>
<dt>p.threshold</dt>
<dd>The minimum P-value required to assign a genotype (dosage)
to a sample; default 0.99 (very stringent). If the P-value for all possible genotypes is less
than p.threshold the sample is assigned genotype NA. Set to 1 to disable
this filter.</dd></dl>

Arguments

DEPRECATED: Function to fit mixture models for series of markers and save the
results to files — saveMarkerModels

<dl>

<dt>...</dt>
<dd>All parameters allowed in the function `fitMarkers()`. For a full description
see the help of that function.</dd>


<dt>p.threshold</dt>
<dd>The minimum P-value required to assign a genotype (dosage)
to a sample; default 0.99 (very stringent). If the P-value for all possible genotypes is less
than p.threshold the sample is assigned genotype NA. Set to 1 to disable
this filter.</dd>

</dl>

saveMarkerModels: DEPRECATED: Function to fit mixture models for series of markers and save the results to files

Description

Usage

Value

Arguments