R/getCorrType.R

In BaderLab/netDx: Network-based patient classifier

#' Counts the relative correlation of (+,+) and (+,-)(-,-) interactions
#' 
#' @param inFile (character): path to interaction networks
#' @param plusID (character) vector of + nodes
#' @param minusID (character) vector of - nodes
#' @return (numeric) mean edge weight for (+,+) and other edges
getCorrType <- function(inFile, plusID, minusID) {
    dat <- read.delim(inFile, sep = "\t", header = FALSE, as.is = TRUE)
    pp_idx <- dat[, 1] %in% plusID & dat[, 2] %in% plusID
    pp_corr <- mean(dat[pp_idx, 3])
    pm_corr <- mean(dat[setdiff(seq_len(nrow(dat)), pp_idx), 3])
    
    return(c(pp_corr, pm_corr))
}