fitPoly_data: Small fitPoly input datasets for testing and examples

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Small fitPoly input datasets for testing and examples

Description

A list with small datasets of four different ploidy levels for testing and examples

Usage

data(fitPoly_data)

Details

list fitPoly_data contains the following items:

• ploidy2: a diploid dataset with only the SNP array signal ratios

• ploidy3: a triploid dataset with in addition to the signal ratios two data.frames specifying the population structure

• ploidy4: a tetraploid dataset similar to the triploid dataset and additionally prior dosage information of the F1 population parents and of a few other samples

• ploidy6: a hexaploid dataset similar to the tetraploid dataset and additionally the 7 starting means for some of the markers

Each of the items contains one or more elements, postfixed by 2x, 3x, 4x or 6x depending on the ploidy:

• dat: a data.frame with at least columns MarkerName, SampleName and ratio with the signal ratios to be analyzed

• pop: a data.frame with columns SampleName and Population, specifying the population to which each sample belongs

• pop.par: a matrix specifying what are the parents of each population (if any)

• parPriors: a data.frame specifying prior known allele dosages for the F1 parents

• sampPriors: a data.frame specifying the prior known dosages for other samples

• startmeans: a data.frame with prior known means for the (ploidy+1) mixture model components

In addition the ploidy6 component has elements pop and pop.parents (no suffix) which are equivalent to pop6x and pop.par6x, in the format required by function codomMarker.

fitPoly documentation built on April 3, 2025, 8:58 p.m.