progeny_haplotypes: Generate data.frame with genotypes estimated by HMM and its probabilities
Description
Generate data.frame with genotypes estimated by HMM and its probabilities
Usage
progeny_haplotypes(..., ind = 1, group_names = NULL, most_likely = FALSE)
Value
a data.frame information: individual (ind) and marker ID, group ID (grp), position in centimorgan (pos),
genotypes probabilities (prob), parents, and the parents homologs and the allele IDs.
Arguments
...
Map(s) or list(s) of maps. Object(s) of class sequence.
ind
vector with individual index to be evaluated or "all" to include all individuals
group_names
Names of the groups.
most_likely
logical; if TRUE, the most likely genotype receive 1 and all the rest 0.
If there are more than one most likely both receive 0.5.
if FALSE (default) the genotype probability is plotted.