changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / rsem-for-ebseq-generate-ngvector-from-clustering-info

diff --git a/rsem-for-ebseq-generate-ngvector-from-clustering-info b/rsem-for-ebseq-generate-ngvector-from-clustering-info
deleted file mode 100755 (executable)
index 312dbfa..0000000
--- a/rsem-for-ebseq-generate-ngvector-from-clustering-info
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env Rscript
-
-argv <- commandArgs(TRUE)
-if (length(argv) != 2) {
-  cat("Usage: rsem-for-ebseq-generate-ngvector-from-clustering-info input_file output_file\n")
-  q(status = 1)
-}
-
-data <- read.table(file = argv[1], stringsAsFactors = F)
-idx <- data[,2] >= 0
-kmr <- kmeans(data[idx, 2], 3)
-order <- order(kmr$centers)
-
-ngvec <- rep(0, length(idx))
-ngvec[idx] <- order[kmr$cluster]
-ngvec[!idx] <- 3
-
-write.table(ngvec, file = argv[2], row.names = F, col.names = F)