Returns filtered msigdb geneset in a format compatible with cross-talks calculations

Download MsidgDB data, filter them and prepare them in the format needed by cross-talks calculation

Usage

pathway_data(
  species,
  category = NULL,
  subcategory = NULL,
  type = "gene_symbol",
  genes,
  min_size = 1,
  max_size = 500
)

Arguments

species: Species name
category: MSigDB category name, see `msigdbr_collections()`
subcategory: MsigDB subcategory name, see `msigdbr_collections()`
type: Gene name of interest, can be `gene_symbol` or `entrez_gene`
genes: vector with gene gene name of interest
min_size, max_size: filtering the gene sets to maintain only the ones that have at least `min_size` or less than `max_size` number of genes

Value

The output is a list of two output:

msigdb_output: a data.frame with the data downloaded by MSigDB data
path_list: a list of pathway. Each list is composed by a vector with the names of the genes of interest that are part of that pathway

Details

The function downloads the pathway data for the `species` of interest. The selection of the database to download is made by using the parameter `category` and `subcategory`. The data downloaded are then filtered to maintain only the `genes` of interest and to remove pathway with a number of genes lower of `min_size` and higher of `max_size`