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pe_size
2012 Aug 24
0
A question about GRAMMAR calculations in the FAM_MDR algorithm
...;)
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
S...