GO_analysis: Gene Ontology (GO) term analysis

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

Description

Gene Ontology (GO) term analysis

Usage

GO_analysis(selected_genes_, all_genes_, organism_, gene_id_type_ = "symbol",
  ontology_ = "CC", verbose_level_ = 1, pvalueCutoff_ = 0.01,
  qvalueCutoff_ = 0.05)

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".
ontology_	Either "MF" (Molecular Function), "CC" (Cellular Component, default), or "BP" (Biological Process).
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.