-#!/usr/bin/env Rscript
-
-printUsage <- function() {
- cat("Usage: rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_of_samples_in_condition_1 FDR_rate output_file\n\n")
- cat("This script calls EBSeq to find differentially expressed genes/transcripts in two conditions.\n\n")
- cat("data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.\n")
- cat("[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.\n")
- cat("number_of_samples_in_condition_1: the number of samples in condition 1. A condition's samples must be adjacent. The left group of samples are defined as condition 1.\n")
- cat("FDR_rate: false discovery rate.\n")
- cat("output_file: the output file. Three files will be generated: 'output_file', 'output_file.hard_threshold' and 'output_file.all'. The first file reports all DE genes/transcripts using a soft threshold (calculated by crit_func in EBSeq). The second file reports all DE genes/transcripts using a hard threshold (only report if PPEE <= fdr). The third file reports all genes/transcripts. The first file is recommended to be used as DE results because it generally contains more called genes/transcripts.\n\n")
- cat("The results are written as a matrix with row and column names. The row names are the genes'/transcripts' ids. The column names are 'PPEE', 'PPDE', 'PostFC' and 'RealFC'.\n\n")
- cat("PPEE: posterior probability of being equally expressed.\n")
- cat("PPDE: posterior probability of being differentially expressed.\n")
- cat("PostFC: posterior fold change (condition 1 over condition2).\n")
- cat("RealFC: real fold change (condition 1 over condition2).\n")
- q(status = 1)
-}
-
-argv <- commandArgs(FALSE)
-path <- dirname(sub("--file=", "", argv[grep("--file", argv)]))
-path <- paste(path, "EBSeq", sep = "/")
-start_pos <- grep("--args", argv) + 1
-end_pos <- length(argv)
-if (start_pos <= end_pos) argv <- argv[start_pos : end_pos] else argv <- NULL
-
-ng_pos <- grep("--ngvector", argv)
-if (length(ng_pos) > 1 || length(ng_pos) == 0 && length(argv) != 4 || length(ng_pos) == 1 && length(argv) != 6) printUsage()
-ngvector_file <- NULL
-if (length(ng_pos) == 1) {
- if (ng_pos == length(argv)) printUsage()
- ngvector_file <- argv[ng_pos + 1]
- argv <- argv[-c(ng_pos, ng_pos + 1)]
-}
-
-data_matrix_file <- argv[1]
-num_con1 <- as.numeric(argv[2])
-fdr <- as.numeric(argv[3])
-output_file <- argv[4]
-
-library(blockmodeling, lib.loc = path)
-library(EBSeq, lib.loc = path)
-
-DataMat <- data.matrix(read.table(data_matrix_file))
-n <- dim(DataMat)[2]
-conditions <- as.factor(rep(c("C1", "C2"), times = c(num_con1, n - num_con1)))
-Sizes <- MedianNorm(DataMat)
-ngvector <- NULL
-if (!is.null(ngvector_file)) {
- ngvector <- as.vector(data.matrix(read.table(ngvector_file)))
-}
-
-
-EBOut <- NULL
-if (is.null(ngvector)) {
- EBOut <- EBTest(Data = DataMat, Conditions = conditions, sizeFactors = Sizes, maxround = 5)
-} else {
- EBOut <- EBTest(Data = DataMat, NgVector = ngvector, Conditions = conditions, sizeFactors = Sizes, maxround = 5)
-}
-stopifnot(!is.null(EBOut))
-
-PP <- as.data.frame(GetPPMat(EBOut))
-fc_res <- PostFC(EBOut)
-
-# soft threshold, default output
-thre <- crit_fun(PP[, "PPEE"], fdr)
-DEfound <- rownames(PP)[which(PP[, "PPDE"] >= thre)]
-
-results <- cbind(PP[DEfound, ], fc_res$PostFC[DEfound], fc_res$RealFC[DEfound])
-colnames(results) <- c("PPEE", "PPDE", "PostFC", "RealFC")
-write.table(results, file = output_file)
-
-# hard threshold
-thre <- 1.0 - fdr
-DEfound <- rownames(PP)[which(PP[, "PPDE"] >= thre)]
-
-results <- cbind(PP[DEfound, ], fc_res$PostFC[DEfound], fc_res$RealFC[DEfound])
-colnames(results) <- c("PPEE", "PPDE", "PostFC", "RealFC")
-write.table(results, file = paste(output_file, ".hard_threshold", sep = ""))
-
-# all
-results <- cbind(PP, fc_res$PostFC, fc_res$RealFC)
-colnames(results) <- c("PPEE", "PPDE", "PostFC", "RealFC")
-write.table(results, file = paste(output_file, ".all", sep = ""))