Description Usage Arguments Details Value Author(s) Examples
Calculates the the Pedigree-based Additive Relationship Matrix. This is twice the pedigree based kinship matrix.
1 |
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.only |
If |
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. |
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). |
Additive relationship matrix.
Robin Wellmann
1 2 3 4 5 6 | 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]
|
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
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