rankProfiles: Ranking profiles of pedigree member
In thoree/inbred: Different functions related to LR, bootstrap etc

Description Usage Arguments Details Value Author(s) Examples

Ranking profiles of pedigree member

1	rankProfiles(x, id, markers = NULL, maxPerMarker = Inf, verbose = FALSE)

`id`	Name of individual to be predicted
`maxPerMarker`	No of top candidates per marker, default all
`Names`	Namesor indices of the markers to be included. By default, all markers.
`A`	logical, by default TRUE

Markers are assumed independent. For each marker, the possible genotypes for 'id' are evaluated and ranked according to how probable they are. It may be wise to try first with 'maxPerMarker = 1' to limit computation time, particularly if mutations are modeled.

A list with three components. The first, a data frame with profiles ranked according to the likelihood. The posterior equals the likely for a prior which gives equal probability to all possible profiles. Then follows the most likely profile. Finally, the second to most likely genotypes are given.

Magnus Dehli Vigeland

library(pedprobr)
x = nuclearPed(2, father = "FA")
m1 = marker(x, "3" = 1, "4" = 1:2, alleles = 1:2, name = "m1")
m2 = marker(x, "3" = 1, "4" = 2, alleles = 1:2, name = "m2")
m3 = marker(x, "3" = 2, "4" = 2, alleles = 1:2, name = "m3")
x = setMarkers(x, list(m1, m2, m3))
id = "FA"
markers = NULL
maxPerMarker = 2
rankProfiles(x, id, markers, maxPerMarker)
rankProfiles(x, id, markers, maxPerMarker = 1)
library(pedmut)
mutmod(x, 1:3) = list(model = "equal", rate = 0.002)
rankProfiles(x, id, markers, maxPerMarker = Inf)