Nothing
kfold.MDscan <-function(iicc,TF){
require("seqinr")
require("MEET")
write.fasta <- get("write.fasta",pos="package:seqinr")
read.fasta <- get("read.fasta",pos="package:seqinr")
k<-length(iicc$DNAreal)
y<-read.fasta(file=TF,forceDNAtolower=FALSE)
y<-y[-iicc$outsequence]
write.fasta(sequences=y,names=c(1:length(y)),file.out="setTF.fa",open="w")
validation.set_x <- iicc$DNAreal
lenmotif<-iicc$lenmotif
len_motif_inici<-(lenmotif-3)
len_motif_final<-(lenmotif+3)
num_motif<-iicc$nummotif
direction<-iicc$direction
call.MDscan<-iicc$MDscan
Scoretotal <- lapply(seq(len_motif_inici,len_motif_final , 1), function(x){})
for (m in c(1:length(y))) {
x<-y[-m]
write.fasta(sequences=x,names=c(1:length(x)),file.out="factor.fa",open="w")
training.set<-switch(iicc$alignment, "CLUSTALW"=align.clustalw(filein="factor.fa", fileout="background.fa", call=iicc$call.clustalw), "MUSCLE"=align.muscle(filein="factor.fa", fileout="background.fa", gapopen=iicc$gapopen, maxiters=iicc$maxiters, gapextend=iicc$gapextend, call=iicc$call.muscle),"MEME"=align.MEME(filein="factor.fa",fileout="background.fa",iicc),"NONE"=Read.aligned("factor.fa"), stop("Alignment method not included"))
for (len_motif in seq(len_motif_inici,len_motif_final,1)){
resultats_MDscan<-run.read.MDscan(validation.set_x,k, len_motif, num_motif, call.MDscan)
Score<-scoreMDscan(resultats_MDscan,k,training.set,direction)
Scoretotal[[len_motif-len_motif_inici+1]]<-rbind( Scoretotal[[len_motif-len_motif_inici+1]],Score)
}
}
SCOREtotal <- lapply(Scoretotal, function(x){as.vector(t(x))})
return(SCOREtotal)
}
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