KEGG_analysis: KEGG pathway analysis

Description Usage Arguments

Description

KEGG pathway analysis

Usage

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KEGG_analysis(selected_genes_, all_genes_, organism_,
  gene_id_type_ = "symbol", ontology_ = "CC", verbose_level_ = 1,
  pvalueCutoff_ = 1, qvalueCutoff_ = 1)

Arguments

selected_genes_

A character vector of genes, by default gene symbols. The ID type can be changed using gene_id_type_ parameter.

all_genes_

A character vector of genes treated as background. It should be a superset of selected_genes_.

organism_

Either "human" or "mouse".

gene_id_type_

Currently either "symbol" (default), or "entrez_id".

verbose_level_

0 for quiet, 1 for simple messages, 2 for additional debug messages.

pvalueCutoff_, qvalueCutoff_

Cutoff threshold for either p or q values.


lanagarmire/NMFEM documentation built on May 20, 2019, 7:34 p.m.