R/enrichment.list.R

In netresponse: Functional Network Analysis

enrichment.list <- function(groupings, annotation.vector) {
    
    annotated.samples <- names(which(!is.na(annotation.vector)))
    annotation.data <- annotation.vector[annotated.samples]
    names(annotation.data) <- annotated.samples
    
    associations <- NULL
    for (sn in names(groupings)) {
        
        mode.samples <- groupings[[sn]]
        
        # annotated samples in the mode
        s <- intersect(mode.samples, annotated.samples)
        
        # annotated samples in other modes
        sc <- intersect(unlist(groupings[setdiff(names(groupings), sn)]), annotated.samples)
        
        if (length(na.omit(s)) > 1 && length(na.omit(sc)) > 1) {
            pvals <- t.test(annotation.data[s], annotation.data[sc])$p.value
            fold.change <- mean(annotation.data[s]) - mean(annotation.data[sc])
        } else {
            warning(paste("Not enough annotated observations for response", sn))
            pvals <- NA
            fold.change <- NA
        }
        
        associations <- rbind(associations, cbind(mode = sn, pvalue = pvals, fold.change = fold.change))
        
    }
    
    associations <- data.frame(list(mode = as.character(associations[, "mode"]), 
        pvalue = as.numeric(associations[, "pvalue"]), fold.change = as.numeric(associations[, 
            "fold.change"])), stringsAsFactors = FALSE)
    
    
    associations
    
}