progeny_haplotypes function

Generate data.frame with genotypes estimated by HMM and its probabilities

progeny_haplotypes(..., ind = 1, group_names = NULL, most_likely = FALSE)

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.

Returns

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.

Examples

data("onemap_example_out")
twopts <- rf_2pts(onemap_example_out)
lg1 <- make_seq(twopts, 1:5)
lg1.map <- map(lg1)
progeny_haplotypes(lg1.map)

Author(s)

Getulio Caixeta Ferreira, getulio.caifer@gmail.com

Cristiane Taniguti, chtaniguti@tamu.edu