| convert_updog {polymapR} | R Documentation |
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)