From 35f5537c0ec7e762a62e260c35bc62da1a155576 Mon Sep 17 00:00:00 2001 From: reednel Date: Wed, 17 Jan 2024 14:27:24 -0600 Subject: [PATCH] readme edit --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 5383ef4..243e277 100644 --- a/README.md +++ b/README.md @@ -50,7 +50,7 @@ This utility has the form `./minaa.exe [-B=bio] [-a=alpha] [-b=beta]`. #### Common - **-B=**: the path to the biological cost matrix file. - - Require: CSV adjacency matrix where the first column consists of the labels of G, in order, and first row consists of the labels of H, in order. + - Require: a CSV adjacency matrix where the first column consists of the labels of G, in order, and first row consists of the labels of H, in order. - Default: the algorithm will run using only topological calculations. - Notes: - The input matrix is normalized by MiNAA such that all entries are in range [0, 1]. @@ -79,16 +79,17 @@ This utility has the form `./minaa.exe [-B=bio] [-a=alpha] [-b=beta]`. - **-p**: passthrough; whether or not to write the input files into the output folder. - Require: none. - Default: the files are not passed through to the output folder. - - Note: The output reflects the input data after having been processed by the algorithm, this is not a direct copy and paste. + - Note: the output reflects the input data after having been processed by the algorithm, this is not a direct copy and paste. - **-t**: timestamp; the output folder's name includes the date and time of execution. - Require: none. - Default: the output folder's name does not include date and time. - **-g**: greekstamp; the output folder's name includes the values for alpha and beta. - Require: none. - Default: the output folder's name does not include the values for alpha and beta. -- **-s**: similarity conversion; for each entry in the given biological matrix, the value (post normalization) is replaced with 1 - value. Use this if and only if the provided biological matrix is a similarity matrix. +- **-s**: similarity conversion; for each entry in the given biological matrix, the value (post normalization) is replaced with 1 - value. - Require: none. - Default: the given biological matrix is left as is. + - Note: use this if and only if the provided biological matrix is a similarity matrix. ### Outputs