Joint continuous multi-Omics enrichment ANAlysis (JOANA) from MLO Lab.
We recommend utilizing conda for environment management, and pip for installing joanapy as a Python package. Follow these instructions to set up and activate joanapy
conda create -n joana python=3.11
conda activate joana
Before installing joanapy try to install mono on your conda environment by the following command
conda install conda-forge::mono
Make sure that your working directory is JOANA-main which you have downloaded. Use pip to install joanapy on your conda environment.
pip install .
after installing joanapy on joana environment run JOANA through run-joana function.
run-joana [-o omics1.txt] [-o2 omics2.txt] [-p pathwayfile.gmt] [-d input-output-directory-path] [-m min-num-genes]
-o input file-name. This file is a two-column tab delimited the first column is gene-name and second column signifficant score (e.g. q-values) coresponde to that gene.
-o2 input file-name in the case of multi-omics the format of this file is also the same as the first file.
-p the file-name of 'gmt' file which contains biological pathways that are going to test for enrichment.
-d specify the path that all the input files are in. Also this path specifies the path of result directory of JOANA.
-m its a number between [0,1) which specified by client (default value is 0). '-m 0.5' means JOANA consider pathways which atleast 50% of its genes have measurments.
The input files -o and -o2 should be a two-column tab-delimited file (make sure files don't contain any header) with the following format:
A2ML1 0.025202476125022
A3GALT2 0.878666355638669
A4GALT 0.983155339235838
A4GNT 0.971337673847852
AAAS 0.0863723498889275
AACS 0.230709278931887
AADAC 0.881216487254285
The 'gmt' file could be downloaded from msigDB or any other desired biological pathway file with gmt format.
To execute JAOAN on single-omics data if you are already in the directory of input data, the command line would be:
run-joana -o omics1.txt -p pathway.gmt -d ./ -m 0.7
And to execute JAOAN on multi-omics data if you are already in the directory of input data, the command line would be:
run-joana -o omics1.txt -o2 omics2.txt -p pathway.gmt -d ./ -m 0.7
Note: When dealing with multi-omics data, the '-o' input file serves as the reference file, and missing values in the second modality '-o2' are handled based on the reference data-modality. It's crucial to select the file with more gene measurements as the reference, as this provides better data integrity and completeness.
An example for how to run JOANA with joanapy can be found in the joanapy/tests folder.
The package can be uninstalled with the following command:
pip uninstall joanapy
Code was adapted from Schröder C, Rahmann S. A hybrid parameter estimation algorithm for beta mixtures and applications to methylation state classification. Algorithms Mol Biol. 2017 Aug 18;12:21. doi: 10.1186/s13015-017-0112-1. PMID: 28828033; PMCID: PMC5563068 (https://bitbucket.org/genomeinformatics/betamix/src/master/).