makeA: Calculates the Pedigree-based Additive Relationship Matrix

Description Usage Arguments Details Value Author(s) Examples

View source: R/makeA.R

Description

Calculates the the Pedigree-based Additive Relationship Matrix. This is twice the pedigree based kinship matrix.

Usage

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makeA(Pedig, keep.only=NULL, keep=keep.only, AFounder=NULL)

Arguments

Pedig

Data frame containing the Pedigree. The data frame has columns (1) Individual, (2) Sire, (3) Dam. Missing parents are coded as NA. Both parents must either be missing or present. If this is not the case use prePed.

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.

AFounder

Additive relationship matrix of 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 additive relationship matrix A which is twice the kinship matrix. For individuals i and j it is defined as

Aij = 2*(Probability that two alleles chosen from individuals i and j are IBD).

Value

Additive relationship matrix.

Author(s)

Robin Wellmann

Examples

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data(PedigWithErrors)
data(Phen)
Pedig <- prePed(PedigWithErrors)
keep  <- Pedig$Indiv[summary(Pedig)$equiGen>5 & Pedig$Indiv %in% Phen$Indiv]
A     <- makeA(Pedig, keep.only=keep)
A[1:3,1:3]

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

                276000812496744 276000891862786 276000812202159
276000812496744      1.00890350      0.02528292      0.09925413
276000891862786      0.02528292      1.01370025      0.02666634
276000812202159      0.09925413      0.02666634      1.02727461

optiSel documentation built on Jan. 16, 2021, 5:30 p.m.