Nothing
`checkATCG` <-
function(mat,first.ref=FALSE){
homo<-c("AA","TT","CC","GG")
hete<-c("AT","TA","AC","CA","AG","GA","TC","CT","TG","GT","CG","GC")
if(!all(mat%in%c(homo,hete,NA)))
stop("All values in mat must be combinations of length 2 of\n",
"the letters A, T, C and G.")
mat.homo<-matrix(0,nrow(mat),4)
for(i in 1:4)
mat.homo[,i]<-rowSums(mat==homo[i],na.rm=TRUE)
if(any(rowSums(mat.homo>0)>2))
stop("At least one of the SNPs shows more than 2 homozygous genotypes.",
call.=FALSE)
if(!first.ref){
for(i in 2*(1:6))
mat[mat==hete[i]]<-hete[i-1]
hete<-hete[2*(1:6)-1]
n.col<-6
}
else
n.col<-12
mat.hete<-matrix(0,nrow(mat),n.col)
for(i in 1:n.col)
mat.hete[,i]<-rowSums(mat==hete[i],na.rm=TRUE)
if(any(rowSums(mat.hete>0)>1))
stop("At least one of the SNPs shows more than 1 heterozygous genotype.",
call.=FALSE)
colnames(mat.hete)<-hete
cs<-colSums(mat.hete)>0
if(any(!cs))
mat.hete<-mat.hete[,cs,drop=FALSE]
mat.hete
}
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