GeneOntology: Gene ontology enrichment analysis for provided gene list

In enrichTF: Transcription Factors Enrichment Analysis

Description

User provide target gene list of forground region. This function will call function for gene ontology enrichment analysis

Usage

enrichGeneOntology(
  prevStep,
  inputTxt = NULL,
  outputTxt = NULL,
  outputPdf = NULL,
  orgDb = NULL,
  keyType = "SYMBOL",
  ...
)

## S4 method for signature 'Step'
enrichGeneOntology(
  prevStep,
  inputTxt = NULL,
  outputTxt = NULL,
  outputPdf = NULL,
  orgDb = NULL,
  keyType = "SYMBOL",
  ...
)

geneOntology(
  inputTxt,
  outputTxt = NULL,
  outputPdf = NULL,
  orgDb = NULL,
  keyType = "SYMBOL",
  ...
)

Arguments

prevStep	Step-class object scalar. This parameter is available when the upstream step function (printMap() to see the previous functions) have been sucessfully called. Accepted value can be the object return by any step function or be feed by %>% from last step function.
inputTxt	Character scalar. Gene list text file. All gene names are in one column.
outputTxt	Character scalar. Gene ontology enrichment analysis result table. Each row contain one gene ontology information.
outputPdf	Character scalar. Gene ontology enrichment analysis result figure. It contains gene ontology network.
orgDb	Character scalar. Bioconductor OrgDb object name for gene ontology enrichment analysis.
keyType	Character scalar. Gene name type include "SYMBOL" and "ENSEMBLE"
...	Additional arguments, currently unused.

Details

Currently, this function call enrichGO from package clusterProfiler to implement this funtion.

Value

An invisible EnrichStep-class object (Step-class based) scalar for downstream analysis.

Author(s)

Zheng Wei

See Also

regionConnectTargetGene enrichRegionConnectTargetGene

Examples

genelist.txt <- system.file(package = "enrichTF", "extdata","genelist.txt")
geneOntology(inputTxt = genelist.txt, orgDb = "org.Hs.eg.db")

enrichTF documentation built on Nov. 8, 2020, 6:15 p.m.