dalloliogm / MEGA

Welcome to MEGA-RVs Repository

1. GNU General Public License ==============================

This repo contains 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 software 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 http://www.gnu.org/licenses/.

2. Repository Description ==========================

MEGA-RVs (Mutation Enrichment Gene set Analysis of Rare Variants) was developed to identify predefined gene sets (e.g. genes involved in the same pathway, or predisposing to specific diseases) that show a significantly higher number of mutations in a group of samples A as compared to another group of samples B.

3. How to use it ================== From Broswer

The easiest way to run MEGA-RVs is to install Shiny package (and the required dependencies) in R, and use the function runGithub(). See the example below,

install.packages("shiny")
install.packages("shinyjs")
install.packages("shinythemes")
install.packages("DT")

library(shiny)
library(shinyjs)
library(plotly)
library(shinythemes)
library(DT)

runGitHub("MEGA","Your_username")

From R shell

inunput: A and B: Boolean matrices of mutations. Coloums are samples, while rows are mutations. The first coloumn must always contain the name of the gene in which the mutation fall.

Example:

1. Load the MEGA-RVs functions in the Global Enviroment
   source("./MEGA.R")
   

2. Load the predifined list of gene sets. As example, here we use KEGG gene sets
   load("./example_dataset/MEGA.example.imput.Rdata")
   

3. Load the two sets of individuals A and B. load("./example_dataset/KEGG.186.gene.sets.Rdata")
   

4. Run MEGA-RVs and identify which gene sets are significanly mutated in the group of samples A as compared to B
   r = MEGA(A,B,gene.sets.kegg)
   

5. A summary with the imput parameters used will be showed befor MEGA-RVs start.

+----------------------------------------+
Input parameters:
FDR threshold: 0.1
Number of Gene Sets: 186
Bootstrapping: YES
Number of iterations: 1000
+----------------------------------------+

Step 1: Enrichement Gene Set Enrichement Anlysis |===============================================| 100%

Step 2: Bootstrapping for 4 significant gene sets |===============================================| 100%

Results: Significant Gene sets before FDR: 26 Significant Gene sets after FDR: 4

6. Show the 4 significant pathways
   head(r,4)