R/cut_by_logit2NES.R

In massiveGST: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test

cut_by_logit2NES <-
function (ttable, logit2NES_threshold = 0.57999999999999996) 
{
    if (is.null(ttable)) {
        message("Empty table.")
        return(NULL)
    }
    if (nrow(ttable) < 1) {
        message("Empty table.")
        return(NULL)
    }
    alternative <- attr(ttable, "alternative")
    wwhich <- switch(alternative, two.sided = which(ttable$abs_logit2NES >= 
        logit2NES_threshold), greater = which(ttable$logit2NES >= 
        logit2NES_threshold), less = which(ttable$logit2NES <= 
        -logit2NES_threshold))
    ttable <- ttable[wwhich, ]
    if (nrow(ttable) < 1) {
        message("No gene-set enriched at level ", logit2NES_threshold)
        ttable <- NULL
    }
    return(ttable)
}