Download and install gact database

Introduction

This tutorial is designed to download and set up the gact database, which is focused on genomic associations for complex traits. The tutorial is structured into two main parts: downloading and installing the database, and then providing an overview of its contents:

# library(devtools)
# devtools::install_github("psoerensen/gact")
# devtools::install_github("psoerensen/qgg")


# Download and install gact database
library(gact)
GAlist <- gact(version="hsa.0.0.1", dbdir="C:/Users/gact", task="download")
saveRDS(GAlist, file="C:/Users/gact/hsa.0.0.1/GAlist_hsa.0.0.1.rds")


# Overview of database content

GAlist <- readRDS(file="C:/Users/gact/hsa.0.0.1/GAlist_hsa.0.0.1.rds")

## GWAS Summary Statistics
GAlist$studies

## Accessing the 'dirs' Slot
GAlist$dirs

## Listing Directories and Files
### All Directories Recursively
list.dirs(GAlist$dirs, recursive = TRUE)

### Files under 'marker' Directory
list.files(GAlist$dirs["marker"])

### Files under 'gstat' Directory
list.files(GAlist$dirs["gstat"])

### Files under 'gsea' Directory
list.files(GAlist$dirs["gsea"])