I intend to obtain kinship matrix from pedigree data through proc inbreed to be used as input to proc mixed in order to obtain additive genetic variance. The warning message is always "Individual clone=I011412 has been previously defined. Observation 27 corresponding to this individual will
not be processed." How do I order individuals to avoid this warning message?
proc inbreed data=pedigree covar outcov=kinmat;
var clone female male;
run;
I have not used SAS for many years so I am not so familiar with it. If you are familiar with R environment, I would recommend you to use the R packages, e.g., pedigree and kinship. These two packages work in R and contain several handy functions to be used. Pedigree package can order animals for in the pedigree. with kind regards, Panya
Hi all,
Sorry it is not what you ask for, but I would also recommend you to use R. I like very much the package MasterBayes to deal with pedigree; orderPed() orders your pedigree appropriately. You can then feed this pedigree directly to models to estimate quantitative genetic parameters (MCMCglmm is my favorite, but it is Bayesian). You can also get the kinship matrix using the package Pedantics and others.
Best,
Timothée
In preparing pedigree files for making a relationship matrix, I use ASREML-R which requires a file which shows "me, mum, dad, Fgen", and the file must be in ancestral order, so that the parents always precede their progeny in the file. The file is converted into an A-matrix using ASREML commands, and added to the data analysis to give estimates of additive and non-additive genetic variance. Don't forget to show the level of inbreeding (selfing) using Fgen. For doubled haploids, I use "10" as the number of generations of selfing (i.e. Fgen = 10). If you are using clones, these are probably not inbred (Fgen = 0). What crop are you analysing?
Cheers, Wallace Cowling
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