library(WGCNA) arg_values <- commandArgs(trailingOnly = TRUE) ParseArgs <- function(args){ trait_vals <- as.numeric(unlist(strsplit(args[1], split=" "))) target_vals <- as.numeric(unlist(strsplit(args[2], split=" "))) return(list(trait_vals= c(trait_vals),target_vals = c(target_vals))) } BiweightMidCorrelation <- function(trait_val,target_val){ results <- bicorAndPvalue(c(trait_val),c(target_val)) return ((c(c(results$bicor)[1],c(results$p)[1]))) } parsed_values <- ParseArgs(arg_values) cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))