Nothing
appnn <- function(sequences) UseMethod("appnn")
appnn.default <- function(sequences){
strsqncs <- .aux$str2char(sequences)
results <- list()
for(i in 1:length(strsqncs)){
results[[i]] <- list()
ncdcsqnc <- .aux$encode(strsqncs[[i]],.aaindex,.mapping)
rawdata <- .nn$classify(.nn, ncdcsqnc)
results[[i]]$sequence <- sequences[i]
results[[i]]$overall <- max(rawdata)
results[[i]]$aminoacids <- .aux$aaprediction(rawdata)
results[[i]]$hotspots <- .aux$hotspotsidentification(results[[i]]$aminoacids)
}
class(results) <- "appnn"
return(results)
}
print.appnn <- function(x, ...){
for(i in 1:length(x)){
cat('\nPrediction: \n')
print(x[[i]])
}
}
plot.appnn <- function(x, indices, ...){
par(mfrow=c(1,length(indices)))
for(i in indices){
plot(x[[i]]$aminoacids, xaxt = "n", main = x[[i]]$sequence, ylab="Propensity", xlab="Sequence",ylim=c(-0.5,1.5))
axis(1, at=1:length(.aux$str2char(x[[i]]$sequence)[[1]]), labels=.aux$str2char(x[[i]]$sequence)[[1]])
lines(x[[i]]$aminoacids)
abline(h=0.5,col=2,lty=2)
}
}
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