basisAnnotate: Annotate the bases of scPNMF

In JSB-UCLA/scPNMF: scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling

Annotate the bases of scPNMF

Description

Perform Gene Ontology (GO) enrichment analysis on each basis to provide biological interpretation

Usage

basisAnnotate(
  W,
  DE_prop = 0.1,
  dim_use = NULL,
  id_type = "SYMBOL",
  ont = "BP",
  OrgDb = "org.Hs.eg.db",
  pvalueCutoff = 0.1,
  qvalueCutoff = 0.1,
  minGSSize = 20,
  maxGSSize = 100,
  simp = FALSE,
  return_fig = FALSE,
  cat_num = 10,
  word_num = 50
)

Arguments

W	The weight matrix from scPNMF.
DE_prop	The proportion of genes to be treated as "DE" genes for GO analysis.
dim_use	Which bases to annotate.
id_type	The gene id types. For example, official gene symbol is SYMBOL. See details in package clusterProfiler.
ont	Which gene ontology to use. One of "BP", "MF" or "CC". The default is "BP".
OrgDb	OrgDb to use.
pvalueCutoff	P-value cutoff on on enrichment tests to report. Default is 0.1.
qvalueCutoff	Q-value cutoff on on enrichment tests to report. Default is 0.1.
minGSSize	Minimal size of genes annotated by Ontology term for testing. Default is 20.
maxGSSize	Maximal size of genes annotated by Ontology term for testing. Default is 100.
simp	If simplifying the GO terms. Default is FALSE.
return_fig	If returning the visualization plots. Default is FALSE.
cat_num	How many GO terms will be shown for basis comparison plot.
word_num	How many GO terms will be used for word cloud plot.

Details

This function annotates the weight matrix W. Each basis of W represents a functional gene cluster. Users can use this annotation to decide which bases should be kept for further analysis. See details about the GO analysis in clusterProfiler.

Author(s)

Dongyuan Song

JSB-UCLA/scPNMF documentation built on July 19, 2023, 10:28 p.m.