In tydarnell/GeneticMediation: An R Package for Causal Mediation Analysis of ROSMAP Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Data

ROSMAP Data

• ReadCounts.csv

• H3K9acDomains.csv

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

UNC Wu Lab Data

• snps.txt

• JulyselGeneBySNP.1030.RData

• mediator_chr#_new.RData (each chr has a separate RData file)

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)

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()

tydarnell/GeneticMediation documentation built on May 17, 2020, 2:33 a.m.