Skip to contents

Build list for cross-talk calculation from MSigDB database list

preparing_msigdb_list.Rd

The function build a gene set list compatible with `gs_cross-talk()` for cross-talk calculation using a desired MSigDB (using msigdbr package)

Usage

preparing_msigdb_list(
  species,
  category = NULL,
  subcategory = NULL,
  type = "gene_symbol",
  genes,
  weights,
  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

weights

vector with `genes` weights in the same order. If `NULL` the function assigns `1` to each gene

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 gene-set list with a vector for each gene-set, composed by weights named after the genes

Details

`preparing_msigdb_list()` uses a MSigDB database to build the list needed by `gs_cross_talk()` for cross-talk calculation. In details, it calls `pathway_data()` function to download the database by using msigdbr package to then build the gene-set list