Displaying 4 results from an estimated 4 matches for "polygen".
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2008 Dec 24
0
command Polygenic gives error message concerning dimensions of data
Dear Sir/Madam,
Since a few day now I try to use the command "polygenic" from the GenAbel
package. However, I keep bumping up against an error message: "Error in
polygenic(Testo, kin = kinship, data = data1) : dimension of outcome and
kinship.matrix do not match".
My data exists of 1240 individuals with 74 markers. It mainly consists of
small fami...
2010 Aug 05
1
an issue about missing data
Hi,
I am using a function 'polygenic' in the package called 'GenABEL'.
--------------------------------------------------------------------------------
> h2.gs <- polygenic(b.dbp~age+age2+age3+sex+b.bmi, kin=gs.gkin, data=gs)
-------------------------------------------------------------------------------
## and I g...
2012 Aug 24
0
A question about GRAMMAR calculations in the FAM_MDR algorithm
...r
missing, 0,1,2 gives count of variant allele
}
# preparing MB-MDR
SNPS = matrix(0,nrow=pedsize,ncol=nsnps)
for (k in 1:nsnps){
SNPS[,k] = allelic(k)
}
SNPS = as.data.frame(SNPS)
SNPS[SNPS==-1] = NA
# GRAMMAR calculations
# here one has to include main effect and/or covariate adjustments in the
polygenic model statement
pkin = kinship(pedigree[,2],pedigree[,3],pedigree[,4])
maineff1 = as.factor(SNPS[,1])
maineff2 = as.factor(SNPS[,2])
Yfit =
polygenic(trait~maineff1+maineff2,pkin,simulation.GenABEL,trait.type="gaussian")
resi = Yfit$pgresidualY
When I calculated the GRAMMAR and ran...
2012 Nov 09
0
Kinship2 and GenABEL
...inship2 to calculate heritabilty, but I would like calculate in
GenABEL too.
I trying the code:
> require(kinship2)
> require(GenABEL)
> pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX,
famid=FID, missid=0))
> kmat = kinship(pedig)
> (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat))
Erro em intI(i, n = d[1], dn[[1]], give.dn = FALSE) :
invalid character indexing
>
How can I calculate heritabilty using GenABEL with kinship matrix of
kinship2 package?
Thanks,
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Silvano Cesar da Cos...