THIS README IS UNDER CONSTRUCTION
A driver script is being built to simplify the use of the software, meanwhile please find a example below :
It is up to you to perform the gene identification, you might want to use the gideon/scripts/genePythia/genePythia.py script ( -h for help) to perform pubmed data mining
After gene identification you must have a database to perform enrichment analyses. This step can be done using the script scripts/step/database_enrichment.R (-h for help)
user@machine:path/to/gideon$ Rscript scripts/step/database_enrichment.R -h
usage: scripts/step/database_enrichment.R [--] [--help] [--opts OPTS] [-i -I [-u -U [-a -A [-o -O [-p -P [-r -R [-t -T
R program designed to perform an enrichment analysis with topology-based annotation. Over-representation analysis is performed according to the parent-child-intersection method. Multi-testing is done with BH and Bonferoni methods on the subset of term with a minimal p-value below 1e-7 by default. P-values are based on combination analysis as described in the parent-child paper using GNU multiple precision arithmetic libraries and their R implementation
flags:
-h, --help show this help message and exit
optional arguments:
-x, --opts OPTS RDS file containing argument values
-i, -i I input gene list return-separated with no header.
-u, -u U universe gene list return-separated with no header.
-a, -a A annotation table. This table is tab delimited with a header (term,genes,type,name,parents). The column genes contains the comma separated list of genes in a term
-o, -o O output prefix
-p, -p P minimum value for pmin (hihgest possible p-value) [default: 1e-7]
-r, -r R regex pattern to remove from gene name [default: -.*]
-t, -t T comma-separated list of type to keep (keep all by default) [default: ]
after enrichment of both A and B gene list you should link results file in a file called config.txt to further analysis
This need to be a tab-separated file with the following header
file: file with enrichment resultsgroup: A or Btitle: title for the annotation spaceannspace: leave NAid: (leave as below) column containing term id in the filedesc: (leave as below) column containing term description in the fileallGenes: (leave as below) column containing all genes of the term in the filegenes: (leave as below) column containing all genes present in both the term and the gene list analyzed in the fileprob: column containing the p-value in the file, unadjusted, BH-adjusted and Boneferonni adjusted p-values are avalableprobMax: Max p-value to keep the termN: (leave as below) column containing the amount of genes in the term in the file
file group title annspace id desc allGenes genes prob probMax N
B/keywords.tab B keywords NA term name genes GI pval 0.05 Ngenes
B/interpro.tab B interpro NA term name genes GI pval 0.001 Ngenes
B/reactome.tab B reactome NA term name genes GI pval 0.05 Ngenes
A/keywords.tab A keywords NA term name genes GI pval 0.1 Ngenes
A/interpro.tab A interpro NA term name genes GI pval 0.005 Ngenes
A/reactome.tab A reactome NA term name genes GI pval 0.1 Ngenes
The final step of gideon is encoded within a R function analyseNetwork_2groups
setwd('.')
conf="config.txt"
genesAFile='A.txt' # list of gene id with no header for group A
genesBFile='B.txt'
genesAUniversFile='universe.txt' # list of gene id with no header that are universe of group A
genesBUniversFile=genesAUniversFile
prefixPatternList=c("-.*") # patterns to remove
genemapping="spid2gneName_map.txt" # tabular file with gene id to gene symbol to have meaningfull network image
source('scripts/step/geneTermLinker_2groups.R')
analyseNetworks_2groups(conf,4,genesAFile,genesBFile,genesAUniversFile,genesBUniversFile,prefixPatternList,printGraph=F,geneMap=genemapping,Glim=0.1,hlim=0.4)
All files in this repository are authored by Julien FOURET and licenced under the GNU Public Licence v3.0
This work have been done during a PhD fellowship co-funded by ViroScan3D and the DGA (Direction Générale de l'Armement) in the context of a CIFRE-Défense
/*
* GIDEON is a software allowing the mining of hidden functional
* relationship between 2 distinct group of genes
*
* Copyright (C) 2018 Julien Fouret
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/