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Introduction Version

TopGO2_GO_enrichment

TASK
Typing name :  TASK.gws_omix.TopGO2GoTerm Brick :  gws_omix v

Performs GO term enrichment using TopGO2 R package

TopGO2-GoTerm class.

A class that wraps the TopGO2 R package for performing GO enrichment analysis on gene list data.

TopGO2 is an open-source R pakage for performing GO enrichment analysis using the Gene Ontology (GO) database.

Alexa A, Rahnenfuhrer J (2022). topGO: Enrichment Analysis for Gene Ontology. R package version 2.50.0.

More information here: https://bioconductor.org/packages/release/bioc/html/topGO.html

[Mandatory]: - Gene list file must contains genes, one per line.

- The gene univers file is a tab-delimited text file format where each row contains
    as a first column gene ID followed by (<TAB>) a list of associated GO term separeted by "," (GO:XXXXXX)

Here's are examples of a Gene Universe File and Gene List File for performing GO term enrichment analysis:

    - Gene list files :
        Gene_0102
        Gene_0708
        ...
        Gene_0909


    - Gene universe file (tab separated) :
        # Gene ontology enrichment analysis
        Gene_0001   GO:0008150, GO:0009987, GO:0016192, GO:0050896
        Gene_0002
        Gene_0003   GO:0050896
        ...
        Gene_2305   GO:001234

    OR .gmt GSEA db files (see documentation here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29 ) :
        # Gene ontology enrichment analysis
        GO:0000001   NA   Gene_00012  Gene_00018  Gene_00019  Gene_00011
        GO:0000002      Here is a description of the gene   Gene_00735  Gene_01257
        GO:0000003   NA   Gene_00012
        ...
        GO:0050896   NA   Gene_00018 Gene_00019

Input

Gene Universe file
A gene universe file containing all annotated genes on the genomic sequence linked to their(s) GO term (see Documentation)
Gene List
Gene list file to assess (see Documentation)

Output

Resource set
A set of resources

Configuration

Gene_universe_format

Gene Universe File format (see Documentation above)

Type : stringAllowed values : gmt_format  topgo_format 

Top_results

Optional

Top X results Fisher's Text p-value based (see TOPGO documentation)

Type : intDefault value : 25