doGo: Do GO?

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Do GO?

Description

Decides whether to do a gene ontologies analysis.

Usage

  doGo(param, seqAnno)
  hasGoAnnotation(seqAnno)

Arguments

param	a list of parameters to extract the logical runGO and the character featureLevel from.
seqAnno	the sequence annotation.

Value

TRUE or FALSE.

Author(s)

Rehrauer, Hubert Schmid, Peter

Examples

  ## Not run: 
    ## FALSE
    param = list()
    param[['refBuild']] = 'Apis_Mellifera/HGSC/build4.5/Annotation/Release_4.5-2017-08-15'
    param[['refFeatureFile']] = 'genes.gtf'
    param = ezParam(param)
    seqAnno <- ezFeatureAnnotation(param, dataFeatureType="gene")
    hasGoAnnotation(seqAnno)
    doGo(param, seqAnno)
    
    ## TRUE
    param = list()
    param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-05-31'
    param[['refFeatureFile']] = 'genes.gtf'
    param = ezParam(param)
    seqAnno <- ezFeatureAnnotation(param, dataFeatureType="gene")
    hasGoAnnotation(seqAnno)
    doGo(param, seqAnno)
  
## End(Not run)

uzh/ezRun documentation built on March 5, 2025, 3:41 p.m.