Nothing
consensus <- function(matali, method = c( "majority", "threshold", "IUPAC", "profile"), threshold = 0.60,
warn.non.IUPAC = FALSE, type = c("DNA", "RNA")){
if(inherits(matali, "alignment")) matali <- as.matrix(matali)
if(!is.matrix(matali)) stop("matrix or alignment object expected")
if(storage.mode(matali) != "character") stop("matrix of characters expected")
method <- match.arg(method)
if(method == "IUPAC"){
type <- match.arg(type)
res <- apply(matali, 2, bma, warn.non.IUPAC = warn.non.IUPAC, type = type)
names(res) <- NULL
return(res)
}
if(method == "majority"){
majority <- function(x) names(which.max(table(x)))
res <- apply(matali, 2, majority)
names(res) <- NULL
return(res)
}
if(method == "profile"){
obsvalue <- levels(factor(matali))
nrow <- length(obsvalue)
row.names(matali)<-NULL
res <- apply(matali, 2, function(x) table(factor(x, levels = obsvalue)))
return(res)
}
if(method == "threshold"){
profile <- consensus(matali, method = "profile")
profile.rf <- apply(profile, 2, function(x) x/sum(x))
res <- rownames(profile.rf)[apply(profile.rf, 2, which.max)]
res <- ifelse(apply(profile.rf, 2, max) >= threshold, res, NA)
names(res) <- NULL
return(res)
}
}
con <- consensus
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.