FitPoly is able to genotype polyploid bi-allelic markers using signalintensities from SNP arrays. ‘fitPoly’ assigns genotypes (alleledosages) to a collection of polyploid samples based on these signalintensities. ‘fitPoly’ replaces the older package ‘fitTetra’ that waslimited to only tetraploid populations whereas ‘fitPoly’ accepts anyploidy level. Version 4.0.0 onwards also include all functionalitiesthat were added in the R package fitPolyTools.
Main functionalities of fitPoly:
fitPoly can fit any ploidy populations following (or not)Hardy-Weinberg equilibrium, F1 populations, with parental or sampleprior information.
Data import from Affymetrix and Illumina SNP arrays into fitPolyformat.
Marker and sample filtering based on signal intensities.
Quality checks using analysis of dosage segregation of F1populations.
Other utiliy functions that can be found in thevignettes.
FitTetra reference:Genotype calling intetraploid species from bi-allelic marker data using mixture models.Voorrips RE, Gort G, Vosman B (2011)
FitTetra 2.0 reference:FitTetra 2.0 – improvedgenotype calling for tetraploids with multiple population and parentaldata support