doEnrichGo: Perform GO enrichment analysis using cluster profiler.

Description Usage Arguments Value

View source: R/doGoEnrichment.R

Description

Perform GO enrichment analysis using cluster profiler.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
doEnrichGo(
  rca.obj,
  annotation = NULL,
  ontology = "BP",
  p.Val = 0.05,
  q.Val = 0.2,
  p.Adjust.Method = "BH",
  gene.label.type = "SYMBOL",
  filename = "GoEnrichment.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

ontology

Either MF, BP, or CC, default BP

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.