get_pathway_enrich: Wrapper: Finds diseases, tumours and tissues associations to...

In LucaGiudice/Simpati: Pathway-based classifier exploits patient similarity network paradigm

Description

Detects "disase type" –> "gene" associations, Detects "disase" –> "gene" associations, Detects "cancer" –> "gene" associations and Detects "tissue" –> "gene" associations

Usage

get_pathway_enrich(
  gene_sets_l,
  key_words,
  disease_type,
  db_disgnet,
  db_cancer_ATLAS,
  db_normal_ATLAS,
  n_cores = 2,
  records_only = TRUE
)

Arguments

gene_sets_l	list of genes
key_words	character vector defining the tumor of interest
disease_type	character vector defining the type of disease to query in disgnet
db_disgnet	disgnet database
db_cancer_ATLAS	human atlas database
db_normal_ATLAS	human atlas database
n_cores	Default 2, number of cores to use in the parallel execution of the function
records_only	Default TRUE, returns only the number of associations and not the information

Details

Detects "disase type" –> "gene" associations with disgnet database and return the ID of the publications confirming the associations for each gene with the user-provided key type

Detects "disase" –> "gene" associations with disgnet database and return the ID of the publications confirming the associations for each gene with the user-provided key type

Detects "cancer" –> "gene" associations with human atlas database and return the ID of the publications confirming the associations for each gene with the user-provided key type

Detects "tissue" –> "gene" associations with human atlas database and return the ID of the publications confirming the associations for each gene with the user-provided key type

Value

Return matrix with the genes information about the tissue in which are involved

LucaGiudice/Simpati documentation built on Jan. 27, 2022, 11:42 p.m.