characterize_gene_set: Given a set of Entrez gene ids, perform KEGG enrichment and...

In ArnaudDroitLab/ef.utils: Eric Utilities

Description

Given a set of Entrez gene ids, perform KEGG enrichment and motif enrichement at the promoters.

Usage

characterize_gene_set(gene.set, annotations.list, skip.motif = FALSE,
  skip.kegg = FALSE, output.dir = "output/", promoter.size = 1000)

Arguments

gene.set	A vector of Entrez IDs representing the genes to be characterized.
annotations.list	A list of annotation databases returned by select_annotations.
skip.motif	If TRUE, motif enrichment is skipped.
skip.kegg	If TRUE, KEGG pathway enrichment is skipped.
output.dir	The directory where output should be stored.A directory for storing output.
file.label	A label for generating file names to save the results. If NULL, results are not saved to disk.

Value

A list containing the characterization results.

ArnaudDroitLab/ef.utils documentation built on Aug. 13, 2019, 9:09 p.m.