Nothing
#############################################################################
# Rearranged oriloc #
# #
# Detection of replication-associated effects on base composition asymmetry #
# #
#############################################################################
rearranged.oriloc <- function(
seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr") ,
g2.coord = system.file("sequences/ct.predict", package = "seqinr") )
{
seq.fasta <- read.fasta(seq.fasta)[[1]]
g2 <- readLines(g2.coord)
g2 <- lapply(g2, function(x) unlist(strsplit(x, split=" ")))
g2 <- lapply(g2, function(x) x[which(x!="")])
start <-as.numeric(unlist(lapply(g2, function(x) x[2])))
end <- as.numeric(unlist(lapply(g2, function(x) x[3])))
strand <- rep("forward",length(start))
strand[which(end<start)] <- "reverse"
meancoord <- (start+end)/2
ncds <- length(start)
gcskew <- numeric(ncds)
atskew <- numeric(ncds)
for(i in seq_len(ncds)){
cds=seq.fasta[start[i]:end[i]]
g3=sum(cds[seq(from=3,to=length(cds),by=3)]%in%c("g","G"))
c3=sum(cds[seq(from=3,to=length(cds),by=3)]%in%c("c","C"))
t3=sum(cds[seq(from=3,to=length(cds),by=3)]%in%c("t","T"))
a3=sum(cds[seq(from=3,to=length(cds),by=3)]%in%c("a","A"))
gcskew[i]=(g3-c3)/(g3+c3)
atskew[i]=(a3-t3)/(a3+t3)
if(is.na(gcskew[i])){
gcskew[i]=0
}
if(is.na(atskew[i])){
atskew[i]=0
}
}
neworder=c(which(strand=="forward"),which(strand=="reverse"))
meancoord.rear <- seq_len(ncds)
gcskew.rear=gcskew[neworder]
atskew.rear=atskew[neworder]
strand.rear=strand[neworder]
meancoord.real=meancoord[neworder]
data=data.frame(meancoord.rear,gcskew.rear,atskew.rear,strand.rear,neworder,meancoord.real)
colnames(data)=c("meancoord.rearr","gcskew.rearr","atskew.rearr","strand.rearr","order","meancoord.real")
return(data)
}
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