This function downloads gene sets from specified Enrichr databases and saves them to a specified output directory as a .tsv file per default. The file is named with a timestamp per default to ensure uniqueness (all databases are stored in a single file). This file has 3 columns: DB containing the database name, Geneset, with the genesets, and Gene, with the gene names.
Usage
download_enrichr_databases(
gene_set_lib,
output_dir = here::here(),
filename = NULL
)Arguments
- gene_set_lib
A character vector of database names to download from Enrichr, for example: c("WikiPathways_2019_Human", "NCI-Nature_2016",)
- output_dir
A string specifying the output directory where the `.tsv` file will be saved. Defaults to the current project directory as defined by `here::here()`.
- filename
Name of the output file (with file extension. Due to commas present in some terms, .tsv is recommended). When left out, the file is named all_databases_timestamp.tsv.
Value
A `data.frame` of gene set annotations with three columns:
- DB
Database name (e.g. `"WikiPathways_2019_Human"`, `"NCI-Nature_2016"`).
- Geneset
The gene set or pathway term from that database.
- Gene
A gene contained in the gene set.
In addition to returning the `data.frame`, the function also writes the same table to disk as a `.tsv` file in the specified `output_dir`.