fitTetra: fitTetra is an R package for assigning tetraploid genotype scores

Package fitTetra contains three functions that can be used to assign genotypes to a collection of tetraploid samples based on bialleleic marker assays. Functions fitTetra (to fit several models for one marker from the data and select the best fitting) or saveMarkerModels (calls fitTetra for multiple markers and saves the results to files) will probably be the most convenient to use. Function CodomMarker offers more control and fits one specified model for a given marker.

Author
Roeland Voorrips and Gerrit Gort
Date of publication
2013-05-28 22:43:11
Maintainer
Gerrit Gort <gerrit.gort@wur.nl>
License
GPL (>= 2.2)
Version
1.0

View on CRAN

Man pages

CodomMarker
Function to fit a mixture model to a vector of signal ratios...
diplo.potato.SNP
SNP data for diploid potato
fitTetra
Function to fit multiple mixture models to signal ratios of a...
fitTetra-package
Fits mixture models for genotype calling in tetraploid...
saveMarkerModels
A function to fit mixture models for series of markers and...
tetra.potato.SNP
SNP data for tetraploid potato

Files in this package

fitTetra
fitTetra/MD5
fitTetra/man
fitTetra/man/tetra.potato.SNP.Rd
fitTetra/man/saveMarkerModels.Rd
fitTetra/man/fitTetra.Rd
fitTetra/man/fitTetra-package.Rd
fitTetra/man/diplo.potato.SNP.Rd
fitTetra/man/CodomMarker.Rd
fitTetra/data
fitTetra/data/tetra.potato.SNP.rda
fitTetra/data/diplo.potato.SNP.rda
fitTetra/data/datalist
fitTetra/R
fitTetra/R/write.files.R
fitTetra/R/wmean2.R
fitTetra/R/wmean.R
fitTetra/R/start.plot.R
fitTetra/R/saveMarkerModels.R
fitTetra/R/save.plot.R
fitTetra/R/padded.R
fitTetra/R/orderpsi.R
fitTetra/R/makeprobs.R
fitTetra/R/loglikf.R
fitTetra/R/length.noNA.R
fitTetra/R/getResultnames.R
fitTetra/R/getPtype.R
fitTetra/R/getPlotsDirectory.R
fitTetra/R/getMutype.R
fitTetra/R/getMuModelNpar.R
fitTetra/R/getMuModelName.R
fitTetra/R/getMuModelInfo.R
fitTetra/R/getModelName.R
fitTetra/R/fitTetra.R
fitTetra/R/fitOneDist.R
fitTetra/R/errorplot.R
fitTetra/R/dnormlogit.R
fitTetra/R/dnormasr.R
fitTetra/R/check.plottype.R
fitTetra/R/calcSelcrit.R
fitTetra/R/PlotHistDensity.R
fitTetra/R/MarkerResult.R
fitTetra/R/EMMax.sd.free.R
fitTetra/R/EMMax.sd.const.R
fitTetra/R/EMMax.sd.R
fitTetra/R/EMMax.p.R
fitTetra/R/EMMax.p.HW.R
fitTetra/R/EMMax.mu.ratiodist.R
fitTetra/R/EMMax.mu.R
fitTetra/R/EMGaussMix.R
fitTetra/R/EMGaussMax.R
fitTetra/R/EMGaussExp.vectorized.R
fitTetra/R/CodomMarker.R
fitTetra/R/ClusterInit.R
fitTetra/NAMESPACE
fitTetra/DESCRIPTION