convert_updog: Convert (probabilistic) genotype calling results from updog...

In polymapR: Linkage Analysis in Outcrossing Polyploids

Convert (probabilistic) genotype calling results from updog to input compatible with polymapR.

Description

Convert (probabilistic) genotype calling results from updog to input compatible with polymapR.

Usage

convert_updog(mout, output_type = "discrete", min_prob = 0.7)

Arguments

mout	An object of class multidog; output of the function multidog.
output_type	Output genotypes can be either "discrete" or "probabilistic", defaults to discrete.
min_prob	If genotypes are being discretised, sets the minimum posterior probability in order to call a genotype with confidence. If maxpostprob < min_prob, that genotype is made missing. A default of 0.7 is suggested with no particular motivation.

Value

If output_type is discrete, the function returns a dosage matrix with rownames given by marker names. Columns are organised as parent 1 genotype, parent 2 genotype and then F1 individuals. If output_type is probabilistic, then the output is a data frame which include columns: MarkerName, SampleName,P0 ~ Pploidy (e.g. P0 ~ P4 for tetraploid, which represents the probability assigning to this dosage), maxgeno (the most likely dosage), and maxP (the maximum probability)

Examples

data("mout")
convert_updog(mout)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.