Nothing
"consensus" <-
function(alignment, cutoff=0.6) {
# Determine the consensus sequence for a given alignment
if(is.list(alignment)) alignment=alignment$ali
aa <- c("V","I","L","M", "F","W","Y", "S","T",
"N","Q", "H","K","R", "D","E",
"A","G", "P","C", "-","X")
composition <- table(alignment)
unk <- composition[!names( composition ) %in% aa]
if(length(unk) > 0) {
warning(paste("\nnon standard residue code:",names(unk),"maped to X"))
for(i in 1:length(unk))
alignment[alignment==names(unk[i])]="X"
}
len <- ncol(alignment)
freq <- matrix(0, nrow = 22, ncol = ncol(alignment),
dimnames = list(aa,seq(1:len)))
for (i in 1:len) {
freq[names(summary((as.factor(toupper(alignment[,i]))))), i] <-
(summary(as.factor(toupper(alignment[,i])))/length(alignment[,i]))
}
cons.freq <- apply(freq[1:20,], 2, max)
cons.tmp <- aa[apply(freq[1:20,], 2, which.max)]
cons.tmp[cons.freq <= cutoff] = "-"
return(list(seq=cons.tmp,
freq=freq,
seq.freq=cons.freq,
cutoff=cutoff))
}
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