Nothing
computeROC_matrix <- function(result, cutoff, DElist, NDElist) {
if (is.null(result@data)) {
result@de <- "NA"
} else {
result@de <- nrow(result@data[result@pval < cutoff, ])
}
ind <- match(DElist, result@id)
DEE <- rep(0, times = length(result@id))
DEE[ind] <- 1
pred <- prediction(1 - result@pval, DEE)
perf <- performance(pred, "tpr", "fpr")
result@roc <- matrix(nrow = length(perf@y.values[[1]]), ncol = 2,
data = NA)
colnames(result@roc) <- c("FPR", "TPR")
result@roc[, 1] <- perf@x.values[[1]]
result@roc[, 2] <- perf@y.values[[1]]
perf <- performance(pred, "prec", "rec")
result@prc <- matrix(nrow = length(perf@y.values[[1]]), ncol = 2,
data = NA)
colnames(result@prc) <- c("Recall", "Precision")
result@prc[, 1] <- perf@x.values[[1]]
result@prc[, 2] <- perf@y.values[[1]]
perf <- performance(pred, "auc")
result@auc <- perf@y.values[[1]]
return(result)
} # end computeROC_matrix
computeROC_list <- function(result, cutoff, DElist, NDElist) {
if (is.null(result@data)) {
result@de <- "NA"
} else {
result@de <- nrow(result@data)
}
ind <- match(DElist, result@id)
DEE <- rep(0, times = length(result@id))
DEE[ind] <- 1
pred <- prediction(result@pval, DEE)
perf <- performance(pred, "tpr", "fpr")
result@roc <- matrix(nrow = length(perf@y.values[[1]]), ncol = 2,
data = NA)
colnames(result@roc) <- c("FPR", "TPR")
result@roc[, 1] <- perf@x.values[[1]]
result@roc[, 2] <- perf@y.values[[1]]
perf <- performance(pred, "prec", "rec")
result@prc <- matrix(nrow = length(perf@y.values[[1]]), ncol = 2,
data = NA)
colnames(result@prc) <- c("Recall", "Precision")
result@prc[, 1] <- perf@x.values[[1]]
result@prc[, 2] <- perf@y.values[[1]]
perf <- performance(pred, "auc")
result@auc <- perf@y.values[[1]]
return(result)
} # end computeROC_list
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