onemap (version 3.2.1)

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.

Author

Getulio Caixeta Ferreira,

Cristiane Taniguti,

Examples

# \donttest{
data("onemap_example_out")
twopts <- rf_2pts(onemap_example_out)
lg1 <- make_seq(twopts, 1:5)
lg1.map <- map(lg1)
progeny_haplotypes(lg1.map)
# }