pedInbreeding: Calculates Pedigree Based Inbreeding

In optiSel: Optimum Contribution Selection and Population Genetics

Description

Calculates Pedigree Based Inbreeding

Usage

pedInbreeding(Pedig)

Arguments

Pedig

Data frame containing the Pedigree with the first 3 columns being Indiv (individual ID), Sire, and Dam, which is usually obtained with function prePed. Missing parents are coded as NA.

Details

Computation of pedigree based inbreeding. This function is a wrapper function for pedigree from package pedigree.

Value

A data frame with column Indiv containing the individual IDs and column Inbr containing the inbreeding coefficients.

Author(s)

Robin Wellmann

Examples

data(PedigWithErrors)
data(Phen)
keep  <- Phen$Indiv 
Pedig <- prePed(PedigWithErrors, keep=keep)
Res   <- pedInbreeding(Pedig)
mean(Res$Inbr[Res$Indiv %in% keep])
#[1] 0.01943394

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Pedigree loops were detected. We recommend to correct them manually before
using prePed(). The parents of the following individuals are set to unknown
to remove the loops.
                           Sire             Dam
276000802875148 276000803622423 276000890878480
276000811476506 276000810087663 276000811476506

The sex of the following animals was not compatible with the pedigree, so
it was modified:
                           Sire             Dam
276000810087663 276000802940621 276000802925028

[1] 0.01943394

optiSel documentation built on March 13, 2020, 3:09 a.m.