User Created Inverse Matrix for Genetic Analysis

From: Michelle <asremlforum_at_VSNI.CO.UK>
Date: Thu, 6 Aug 2009 17:50:31 +0100


I have recently installed ASReml for R in Linux (Suse 11.1) and am attempting to do a genetic analysis (mixed model analysis) of some data and have been following the information provided in Chapter 5 of the ASReml-R instruction manual.

 What I would like to do, is incorporate an inverted genomic relationship matrix which I have already created instead of using an inverted matrix generated from the pedigree (created using asreml.Ainverse() as I understand it). From what I can tell, this is possible, but I am not sure if I am doing it correctly. This is what I have created so far that is generating some data:

RMATINV.giv = read.table(file.choose(), header=FALSE) #inverted matrix
testgeno = read.table(file.choose(), header=TRUE) #genotypes with phenotypes file
test.ped = read.table(file.choose(), header=TRUE) #pedigree file


RMATINV2.giv = as.matrix(RMATINV.giv)
colnames(RMATINV2.giv) = c("9001":"9010")
rownames(RMATINV2.giv) = c("9001":"9010")

test.asr = asreml(Fert ~ ARS.BFGL.BAC.10172, random= ~ giv(Animal,var=T), control = asreml.control(ginverse=list(Animal=RMATINV2.giv)), data=testgeno)

My questions are:

1) the pedigree file does not seem to be incorporatted into the analysis- is this ok and correct?
2) the format of my relationship matrix is a 10 by 10 matrix (not the default format of asreml which likes a row column value format.) It seems that it is ok and possible to leave the matrix in this format as long as this is indicated in control = asreml.control(ginverse=list(Animal=RMATINV2.giv)) as I have done. Is this correct?
3) Also, it is noted in the ASReml-R manual that all forms of an imported inverted matrix need to have a "rowNames" indicator...I'm not sure if I have done this.

Files mentioned in the above code are attached. Thanks to anyone who can provide some information on this subject.


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Received on Fri Aug 06 2009 - 17:50:31 EST

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