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;
download the file by copy/pasting this URL into your browser: https://github.com/ftwkoopmans/goat/raw/main/analyses/goat_manuscript_datasets.rda
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"]]
download_goat_manuscript_data(output_dir, ignore_cache = FALSE)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
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
boolean, set to TRUE to force re-download and ignore cached data, if any. Default: FALSE