KEGG_analysis: KEGG pathway analysis

In lanagarmire/NMFEM: Non-negative Matrix Factorization analysis and module generation for scRNA-Seq data

Description

KEGG pathway analysis

Usage

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.