X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rsem-for-ebseq-generate-ngvector-from-clustering-info;fp=rsem-for-ebseq-generate-ngvector-from-clustering-info;h=312dbfa33c77339b530e67362e14e391e75f4259;hb=4496388fd52d4354c746f36b1998477f31c2b0dd;hp=0000000000000000000000000000000000000000;hpb=9210a5fece7ec2854eb834d5b2dcbe2d12fbebf1;p=rsem.git

diff --git a/rsem-for-ebseq-generate-ngvector-from-clustering-info b/rsem-for-ebseq-generate-ngvector-from-clustering-info
new file mode 100755
index 0000000..312dbfa
--- /dev/null
+++ b/rsem-for-ebseq-generate-ngvector-from-clustering-info
@@ -0,0 +1,18 @@
+#!/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)