From 6f993eb1b1874300f817af249ed5dfb0b4d47b48 Mon Sep 17 00:00:00 2001 From: Amin Emad Date: Tue, 30 May 2017 13:24:17 -0500 Subject: [PATCH] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5233c06..a2df313 100644 --- a/README.md +++ b/README.md @@ -102,5 +102,5 @@ To test whether ProGENI runs as expected on your machine, you can use the sample python3 ProGENI.py gene_expr_sample.csv response_sample.csv network_sample.csv -nr 2 ``` # Running ProGENI_simplified -ProGENI_simplified.py provides a simplified implementation of ProGENI. In this variation, the Pearson correlation coefficient of network transformed gene expressions and phenotype is used to rank the genes. In other words, the steps involving identification of a RCG set and ranking genes in the network with respect to the RCG are removed. +ProGENI_simplified.py provides a simplified implementation of ProGENI. In this variation, the Pearson correlation coefficient of network transformed gene expressions and phenotype is used to rank the genes. In other words, the steps involving identification of a RCG set and ranking genes in the network with respect to the RCG are removed. This method is called "ProGENI-PCC" in the manuscript. Usage of this variation is very similar to ProGENI.py, except that -nr and -pr do not need to be provided.