Cluster_enrichment: Gene ontology on RT clusters using clusterprofiler

In CL-CHEN-Lab/User_interface_for_Kronos_scRT: R-package and Shiny App interface for the analysis of single cell replication timing data

Gene ontology on RT clusters using clusterprofiler

Description

Gene ontology on RT clusters using clusterprofiler

Usage

Cluster_enrichment(
  clusters,
  genes,
  orgDB,
  ontology = c("BP", "MF", "CC", "ALL"),
  showCategory = 10,
  qvalueCutoff = 0.05,
  ...
)

Arguments

clusters,	clusters from RT_clustering
genes,	either a dataframe containing chr,start,end,gene column, where gene is an ENSEMBL identifier or the path to a gtf file
orgDB,	OrgDb.
ontology,	One of "BP", "MF", and "CC" sub-ontologies, or "ALL" for all three.
showCategory,	number of categories to show per cluster
qvalueCutoff,	cut-off for qval
...,	other parameters to pass to enrichGO

Value

ggplot

CL-CHEN-Lab/User_interface_for_Kronos_scRT documentation built on Aug. 1, 2022, 2:08 p.m.