pedIBD: Calculates the Pedigree-based Kinship Matrix

Description Usage Arguments Details Value Author(s) Examples

Description

Calculates the pedigree based probability of alleles to be IBD. This pedigree based kinship matrix is also called coancestry matrix and is half the additive relationship matrix.

Usage

1
pedIBD(Pedig, keep.only=NULL, keep=keep.only, kinFounder=NULL)

Arguments

Pedig

Data frame containing the pedigree with Indiv (individual ID), Sire, and Dam in the first 3 columns. Missing parents are coded as NA. Both parents must either be missing or present. If this is not the case use function prePed to prepare the pedigree.

keep

If keep is provided then kinships are computed only for these animals and their ancestors.

keep.only

If keep.only is provided then kinships are computed only for these animals.

kinFounder

Kinship matrix for the founders. The row names are the ids of the founders. By default, founders are assumed to be unrelated. Founders not included in this matrix are also assumed to be unrelated.

Details

Computation of pedigree based kinship matrix f which is half the additive relationship matrix. For individuals i and j it is defined as

fij = Probability that two alleles chosen from individuals i and j are IBD.

Value

Kinship matrix.

Author(s)

Robin Wellmann

Examples

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data(PedigWithErrors)
data(Phen)
keep  <- Phen$Indiv
Pedig <- prePed(PedigWithErrors, keep=keep, thisBreed="Hinterwaelder", lastNative=1970)
pedA  <- pedIBD(Pedig, keep.only=keep)

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

optiSel documentation built on May 1, 2019, 10:29 p.m.