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

Description Usage Arguments Value

View source: R/AnnotationHelper.R

Description

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

Usage

1
2
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 June 19, 2018, 8:26 p.m.