" class="reference-link">Genetic Mediation

An R Package for Causal Mediation Analysis of ROSMAP Data

Overview

GeneticMediation was created as part of the UNC Wu
Lab project Constructing Causal
Mediation Pathways For Multi-Level Genomic Data

GeneticMediation provides methods for cleaning and processing data
from the ROSMAP study and preparing it for causal mediation analysis.

The documentation pdf can be viewed
here

Installation

You can install GeneticMediation from GitHub
with:

# install.packages("devtools")
devtools::install_github("tydarnell/GeneticMediation")

Prerequisites

####################################################################################
#   
#   Software:--------------------------------------------------------
#
#     R version >= 3.6.1
#     devtools (to install GeneticMediation package from github)
#     Rstudio  (highly recommended)
#
#   Data:------------------------------------------------------------
#
#     ROSMAP Study:**************************************************
#       ReadCounts.csv   
#       H3K9acDomains.csv 
#
#     UNC Wu Lab:****************************************************
#       snps.txt
#       JulyselGeneBySNP.1030.RData
#       mediator_chr#_new.RData (each chr has a separate RData file)
#
####################################################################################

Data Access

• The ROSMAP data can be obtained from
  Synapse. Read
  instructions for data
  access

• The UNC Wu Lab data requires
  permission from Dr. Di Wu

Setup

1) Create an Rproject in Rstudio

2) Install and load GeneticMediation from
GitHub with:

# devtools::install_github("tydarnell/GeneticMediation")
library(GeneticMediation)

3) Create subdirectories of your Rproject directory: data,
data/mediator, results with:

GeneticMediation::setup_folders()

4) Put all data except for the mediator_chr#_new.RData files in the
data folder

5) Put the mediator_chr#_new.RData files in the mediator folder

6) Check that data files are in the data folder with:

GeneticMediation::check_data()