Dear R developers:
I am a PHD candidate student in the school of public health of Peking
University and my major is genetic epidemiology. I am learning the FAM-MDR
algorithm, which is used to detect the gene-gene and gene-environment
interactions in the data of pedigree. The codes were written by Tom
Cattaert of the University of Liege. The algorithms and the sample datasets
are available at
http://www.statgen.ulg.ac.be/index.php?option=com_content&view=article&id=90&Itemid=85.
The R I used is R-2.15.1 in the Windows XP system.
The command lines I have run are as follows:
# data files
pedfile="pedigree1.ped"
phenofil="pheno1.dat"
mapfile="simulation.map"
# solver settings
npermute = 1000 # fixed number of permutations, 1000 is
recommended
alpha = 0.05 # type-I error
Pval = 0.1 # significance level at first step of
mbmdr
set.seed(1982) # for reproducibility
# loading libraries and code
library(kinship2)
library(GenABEL)
source("mbmdr_gaussian.r")
# removing all possible existing files first as a safety measure
file.remove("permoutput.txt")
file.remove("simulation.raw")
file.remove("permuted.txt")
file.remove("permchisq.txt")
file.remove("rawoutput.txt")
# loading data and bringing in GenABEL format
rawfile="simulation.raw"
convert.snp.ped(pedfile, mapfile, rawfile)
simulation.GenABEL = load.gwaa.data(phenofile = phenofil, genofile =
rawfile, force=F,makemap=F,sort=F)
pedigree=read.table(pedfile)
pedsize=nrow(pedigree)
nsnps=(ncol(pedigree)-6)/2
# minor allele count and handling missing genotype data
allelic = function(k){
geno=pedigree[,(5+2*k):(6+2*k)]
allelic=rowSums(geno==2)-(geno[,1]==0 & geno[,2]==0) # -1 for
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 the command, "*Yfit =
polygenic(trait~maineff1+maineff2,pkin,simulation.GenABEL,trait.type="gaussian")
*", the software gave an error alert as "*Error in polygenic(trait ~
maineff1 + maineff2, pkin, simulation.GenABEL, : subscript out of bounds *".
I have tried to solve the problem by checking all the commands written
above and the datasets created before. I assume the reason of the problem
is that the "pkin" file is a 994*994 matrix, while "simulation.GenABEL" is
a data frame of 994 subjects and 10 SNPs. The dimentions of the two files
are different, so "subscript out of bounds". However, I don't know how to
solve the problem. I have sent the messege to the authors of FAMMDR, but
have got no reply. So I hope the developers of R can give me some help.
Best regards
Jinwei Wang
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