lumpAlleles {pedprobr}

Allele lumping

Description

Perform allele lumping (i.e., merging unobserved alleles) for all markers attached to the input pedigree.

Usage

lumpAlleles(x, markers = NULL, always = FALSE, verbose = FALSE)

Arguments

x

A ped object or a list of such.

markers

A vector of names or indices referring to markers attached to x. (Default: All markers.)

always

A logical. If TRUE, lumping is always attempted. By default (FALSE) lumping is skipped for markers where all individuals are genotyped.

verbose

A logical.

Value

An object similar to x, but whose attached markers have reduced allele set.

Examples

x = nuclearPed() |> addMarker(geno = c("1/1", NA, NA), alleles = 1:4)

# Before lumping
afreq(x, 1)

# Lump
y = lumpAlleles(x, verbose = TRUE)
afreq(y, 1)