autoGO: autoGO

In isabellagrassucci/autogo_cp: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations

autoGO

Description

Perform enrichment analysis on all the desired gene lists. This function take advantage of the 'enrichR' package.

Usage

autoGO(
  list_of_genes,
  dbs = c("GO_Molecular_Function_2021", "GO_Cellular_Component_2021",
    "GO_Biological_Process_2021", "KEGG_2021_Human"),
  my_comparison,
  ensembl = F,
  excel = F,
  where_results = "./",
  outfolder = "results/",
  my_autoGO_dir = "~/"
)

Arguments

list_of_genes	it can be a list of dataframe (i.e. the output of read_gene_list()), a vector or a dataframe containing a list of genes or a path to the .txt file.
dbs	Databases over which the enrichment will be performed, based on the enrichR libraries. Default are GO_Molecular_Function_2021, GO_Cellular_Component_2021, GO_Biological_Process_2021, KEGG_2021_Human.
my_comparison	Name of the comparison the user would like to inspect.
ensembl	(Default = FALSE). Set to TRUE if the provided gene list contains Ensembl IDs. A conversion to HGNC will be performed.
excel	(Default = FALSE). Set to TRUE if you want to save output tables in .xlsx format.
where_results	Specify the folder in which you want to save the outputs. Default is "./". Note: if you are working with RNotebook the default working directory, if not specified, is the folder in which the .Rmd file is saved.
outfolder	The name to assign to the folder in which outputs are saved. Default is: "results/". NOTE: please add "/" at the end.
my_autoGO_dir	where have you cloned the auto-go repository, default is your home directory "~/"

isabellagrassucci/autogo_cp documentation built on April 10, 2022, 12:05 a.m.