Nothing
read.vhica <-
function (gene.fasta=NULL, target.fasta=NULL, cb.filename=NULL, div.filename=NULL,
reference = "Gene", divergence = "dS", CUB.method="ENC", div.method="LWL85", div.pairwise=TRUE, div.max.lim=3, species.sep="_", gene.sep=".", family.sep=".", ...)
{
stopifnot(
!(is.null(gene.fasta) && is.null(target.fasta)) ||
!(is.null(cb.filename) && is.null(div.filename)))
vhica.obj <- list()
if (!is.null(gene.fasta)) {
vhica.obj$cbias <-
.seq.codon.bias(gene.fasta=gene.fasta, target.fasta=target.fasta, method=CUB.method, species.sep=species.sep, family.sep=family.sep)
vhica.obj$div <-
.seq.divergence(sequence.fasta=c(gene.fasta, target.fasta), method=div.method, pairwise=div.pairwise, max.lim=div.max.lim, species.sep=species.sep, family.sep=family.sep)
if (!is.null(cb.filename))
write.table(vhica.obj$cbias, file=cb.filename, sep="\t", quote=FALSE, row.names=TRUE)
if (!is.null(div.filename))
write.table(vhica.obj$div, file=div.filename, sep="\t", quote=FALSE, row.names=FALSE)
} else {
vhica.obj$cbias <- .read.codon.bias(file = cb.filename, reference = reference)
vhica.obj$div <- .read.divergence(file = div.filename, divergence = divergence)
}
vhica.obj$reg <- .reference.regression(vhica.obj$cbias, vhica.obj$div,
reference = reference, divergence = divergence, family.sep=family.sep, ...)
vhica.obj$reference <- reference
tmp.target <- levels(vhica.obj$cbias[, "Type"])
vhica.obj$target <- tmp.target[tmp.target != reference][1]
vhica.obj$divergence <- divergence
vhica.obj$family.sep=family.sep
class(vhica.obj) <- c("vhica", class(vhica.obj))
return(vhica.obj)
}
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