doEnrichKEGG: Perform KEGG enrichment analysis using cluster profiler.

In linquynus/RCAv2-beta: Reference Component Analysis

Description

Perform KEGG enrichment analysis using cluster profiler.

Usage

doEnrichKEGG(
  rca.obj,
  annotation = NULL,
  org = "hsa",
  key = "kegg",
  p.Val = 0.05,
  q.Val = 0.2,
  p.Adjust.Method = "BH",
  gene.label.type = "SYMBOL",
  filename = "KEGG_Enrichment.pdf",
  background.set = "ALL",
  background.set.threshold = NULL,
  n.Cells.Expressed = NULL,
  cluster.ID = NULL,
  deep.split = NULL
)

Arguments

rca.obj	An RCA2 object
annotation	An ontology dataset that can be obtained from bioconductor. Used for ID matching.
org	Supported organism in KEGG. An overview is listed in 'http://www.genome.jp/kegg/catalog/org_list.html'. Default: hsa (human)
key	one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot', Default: KEGG.
p.Val	p-value cut-off, default 0.05
q.Val	q-value cut-off, default 0.2
p.Adjust.Method	p-value adjustment method to be used, default BH
gene.label.type	Type of gene.labels used, default SYMBOL
filename	postfix of the plots generated, GoEnrichment.pdf
background.set,	ALL indicates that all genes are considered, CLUSTER indicates that only genes with the cluster of interest are considered (default: ALL)
background.set.threshold,	minimum expression threshold used for mean gene-expression. Either a numerical value or one of the following thresholds computed on the mean gene-expression values across all genes within a considered cluster: Min, 1stQ, Mean, Median, 3rdQ. Default: NULL
n.Cells.Expressed	Alternative threshold to filter genes. Keep only genes that are expressed in at least n.Cells.Expressed cells
cluster.ID	ID of a cluster for which the GO enrichment should be computed. If this is not provided, enrichment will be computed for all clusters. Default: NULL
deep.split	Deep.split to be used if hierachical clustering was used to cluster the projection

Value

RCA object.

linquynus/RCAv2-beta documentation built on Aug. 9, 2020, 12:34 a.m.