Nothing
consensusG<-function (GdP, cat.levels = NULL, gmax=FALSE, het=FALSE)
{
Gid <- GdP$id[-duplicated(GdP$id) == FALSE]
G <- lapply(GdP$G, function(x) {
x[-which(duplicated(GdP$id) == TRUE)]
})
G<-lapply(G, function(x){
x[which(is.na(x)==FALSE)]<-NA
x}
)
if (is.null(cat.levels)) {
cat.levels <- 1
GdP$categories <- rep(1, length(GdP$id))
}else{
if (any(GdP$categories %in% cat.levels == FALSE)) {
stop("some GdP$categories not appearing in cat.levels")
}
}
for (i in 1:length(G)) {
if(gmax){
nG<-tapply(GdP$G[[i]],GdP$id, function(x){
ngs<-table(as.character(x))
if(length(ngs)>0){
if(length(which(ngs==max(ngs)))==1){
names(ngs)[which.max(ngs)]
}else{
NA
}
}else{
NA
}
})
G[[i]][match(names(nG), Gid)]<-as.genotype(c(nG))
}
miss<-is.na(GdP$G[[i]])*(1e+10)
ehet<-homozygote(GdP$G[[i]])*(het*100)
ehet[which(is.na(ehet))]<-0
ecat<-match(GdP$categories, cat.levels)
nG <- GdP$G[[i]][order(miss+ehet+ecat)]
nid <- GdP$id[order(miss+ehet+ecat)]
nG <- nG[-duplicated(nid) == FALSE]
nid <- nid[-duplicated(nid) == FALSE]
nG <- nG[match(Gid, nid)]
G[[i]][which(is.na(G[[i]]))] <- nG[which(is.na(G[[i]]))]
}
GdataPed(id = Gid, G = G, perlocus = GdP$perlocus, marker.type = GdP$marker.type)
}
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