merge_enrich_terms-methods: Merge enriched GO terms.

In abrionne/ViSEAGO: ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity

Description

combine results from GO enrichment tests obtained with topGO package, for a given ontology (MF, BP, or CC).

Usage

merge_enrich_terms(Input)

## S4 method for signature 'list'
merge_enrich_terms(Input)

Arguments

Input

a list containing named elements. Each element must contain the name of topGOdata-class object created by create_topGOdata method and the associated topGOresult-class object(s).

Details

This method extracts for each result of GO enrichment test (topGOresult-class object) and corresponding GO annotations (topGOdata-class object): informations about GO term (identifiant, name, and description), gene frequency (number of significant genes / Annotated genes), pvalue, -log10(pvalue), significant genes identifiants (GeneID, or Ensembl ID, or uniprot accession), and gene symbols. At the last, this method builds a merged data.table of enriched GO terms (p<0.01) at least once and provides all mentionned columns.

Value

an enrich_GO_terms-class object.

References

Alexa A and Rahnenfuhrer J (2016). topGO: Enrichment Analysis for Gene Ontology. R package version 2.28.0.

Matt Dowle and Arun Srinivasan (2017). data.table: Extension of data.frame. R package version 1.10.4. https://CRAN.R-project.org/package=data.table

Herve Pages, Marc Carlson, Seth Falcon and Nianhua Li (2017). AnnotationDbi: Annotation Database Interface. R package version 1.38.0.

See Also

Other GO_terms: GOcount, GOterms_heatmap, annotate, create_topGOdata, gene2GO-class

Examples

###################
# load genes identifiants (GeneID,ENS...) universe/background (Expressed genes)
background_L<-scan(
    system.file(
        "extdata/data/input",
        "background_L.txt",
        package = "ViSEAGO"
    ),
    quiet=TRUE,
    what=""
)

###################
# load Differentialy Expressed (DE) gene identifiants from files
L_pregnantvslactateDE<-scan(
    system.file(
        "extdata/data/input",
        "L_pregnantvslactateDE.txt",
        package = "ViSEAGO"
    ),
    quiet=TRUE,
    what=""
)

L_virginvslactateDE<-scan(
    system.file(
        "extdata/data/input",
        "L_virginvslactateDE.txt",
        package = "ViSEAGO"
    ),
    quiet=TRUE,
    what=""
)

L_virginvspregnantDE<-scan(
    system.file(
        "extdata/data/input",
        "L_virginvspregnantDE.txt",
        package="ViSEAGO"
    ),
    quiet=TRUE,
    what=""
)
## Not run: 
###################
# create topGOdata for BP for each list of DE genes
BP_L_pregnantvslactate<-ViSEAGO::create_topGOdata(
    geneSel=L_pregnantvslactateDE,
    allGenes=background_L,
    gene2GO=myGENE2GO,
    ont="BP",
    nodeSize=5
)

BP_L_virginvslactate<-ViSEAGO::create_topGOdata(
    geneSel=L_virginvslactateDE,
    allGenes=background_L,
    gene2GO=myGENE2GO,
    ont="BP",
    nodeSize=5
)

BP_L_virginvspregnant<-ViSEAGO::create_topGOdata(
    geneSel=L_virginvspregnantDE,
    allGenes=background_L,
    gene2GO=myGENE2GO,
    ont="BP",
    nodeSize=5
)

###################
# perform TopGO tests
elim_BP_L_pregnantvslactate<-topGO::runTest(
    BP_L_pregnantvslactate,
    algorithm ="elim",
    statistic = "fisher"
)

elim_BP_L_virginvslactate<-topGO::runTest(
    BP_L_virginvslactate,
    algorithm ="elim",
    statistic = "fisher"
)

elim_BP_L_virginvspregnant<-topGO::runTest(
    BP_L_virginvspregnant,
    algorithm ="elim",
    statistic = "fisher"
)

###################
# merge topGO results
BP_sResults<-ViSEAGO::merge_enrich_terms(
    Input=list(
        L_pregnantvslactate=c("BP_L_pregnantvslactate","elim_BP_L_pregnantvslactate"),
        L_virginvslactate=c("BP_L_virginvslactate","elim_BP_L_virginvslactate"),
        L_virginvspregnant=c("BP_L_virginvspregnant","elim_BP_L_virginvspregnant")
    )
)

## End(Not run)

abrionne/ViSEAGO documentation built on June 13, 2019, 2:27 p.m.