Data file format for mixed model with pedigree

Hi-

I have a simple question about the setup of the data file when doing a mixed model analysis using the asreml.Ainverse() function on a pedigree file.

PedMGS.ped <- read.table("Ped3MGSBEST.xls",header=TRUE)
#This is the pedigree file. It looks like:
Animal Sire MGS(maternal grand sire)
MGS1 0 0
MGS2 0 0
Sire3 0 0
Sire4 0 0
MGS3 0 0
MGS4 0 0
Sire1 Sire3 MGS3
Sire2 Sire4 MGS4
Animal1 Sire1 MGS1
Animal2 Sire2 MGS2

geno = read.table("geno", header=TRUE)
#This is the phenotype and genotype file. Rec is the breeding record. It looks like:
Animal Fertility Rec SNP 1 SNP2 SNP3 etc...
MGS1 NA 0 NA NA NA
MGS2 NA 0 NA NA NA
Sire3 NA 0 NA NA NA
Sire4 NA 0 NA NA NA
MGS3 NA 0 NA NA NA
MGS4 NA 0 NA NA NA
Sire1 NA 0 NA NA NA
Sire2 NA 0 NA NA NA
Animal1 -1.236 354 0 0 1
Animal2 -0.241 121 1 2 0

Finally, the analysis looks like:

PedMGS.ainv <- asreml.Ainverse(PedMGS.ped, mgs=TRUE)$ginv
attr(PedMGS.ainv,"rowNames")
 test.asr = asreml(Fert ~ SNP1, random= ~ ped(Animal,var=T), ginverse=list(Animal=PedMGS.ainv), data=geno, weights = Rec)

My question is:

Does the setup of the data file with phenotype and genotype records look correct? In this setup I've accounted for all animals listed in the pedigree file even if there are no records for that animal. Is that the correct thing to do? Or is it correct to only list animals with records even though these animals are listed in the pedigree file...like this:

Animal Fertility Rec SNP 1 SNP2 SNP3 etc...
Animal1 -1.236 354 0 0 1
Animal2 -0.241 121 1 2 0

Any help would be much appreciated. Any information I found on this topic was from Chapter 5 of the asreml-R help manual.

Thanks

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Received on Wed Sep 08 2009 - 22:10:54 EST