download_goat_manuscript_data {goat}

Download the datasets that were used in the GOAT manuscript

Description

Downloads OMICs-based datasets that were used in the GOAT manuscript from the GOAT GitHub page. This file is cached in the output directory and only needs to be downloaded once. Multiple datasets are included and their names include the respective PubMed identifiers (PMID).

If you encounter technical difficulties, try to;

1. download the file by copy/pasting this URL into your browser: https://github.com/ftwkoopmans/goat/raw/main/analyses/goat_manuscript_datasets.rda

2. load the data in R using the following 2 lines of code, here assuming you stored the downloaded file at C:/data/goat_manuscript_datasets.rda

load("C:/data/goat_manuscript_datasets.rda")

genelist = goat_manuscript_datasets.rda[["Wingo 2020:mass-spec:PMID32424284"]]

Usage

download_goat_manuscript_data(output_dir, ignore_cache = FALSE)

Arguments

output_dir

full path to the directory where the downloaded files should be stored. Directory is created if it does not exist. e.g. output_dir="~/data" on unix systems, output_dir="C:/data" on Windows, or set to output_dir=getwd() to write output to the current working directory

ignore_cache

boolean, set to TRUE to force re-download and ignore cached data, if any. Default: FALSE

Value

a list of genelist data tables. The names of the list represent the datasets, values in the list are data tables that can be used as a "genelist" in the GOAT R package