This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.
This pull request fixes a few bugs in Garnet's motif_regression.py:
Use the p-value to filter significant motifs in the Garnet output HTML file when a p-value threshold was specified in the config file. Previously the q-value was always used.
Respect the savePlot config file setting. Previously plots were erroneously always saved.
Updated README to make it clear that Forest prizes from Garnet are -log2 transformed, not -log10 transformed.
I'll leave this open for a few days for comments and merge if there are not any.
I suggest we update the Omics Integration version number after merging this. There have been many bug fixes and almost 100 commits since v0.2.
This pull request fixes a few bugs in Garnet's
motif_regression.py:savePlotconfig file setting. Previously plots were erroneously always saved.I'll leave this open for a few days for comments and merge if there are not any.
I suggest we update the Omics Integration version number after merging this. There have been many bug fixes and almost 100 commits since v0.2.