fagroupstopgo_class {FoldGO} | R Documentation

## S4 class for FuncAnnotGroupsTopGO object

### Description

This function conducts functional enrichment analysis for sets of genes generated by `GeneGroups` function.

### Constructor

`FuncAnnotGroupsTopGO(groups, namespace, customAnnot, annot, bggenes, ...)`, where:

  `groups` - object of `GeneGroups` class

  `namespace` - character string specifing GO namespace ("BP", "MF" or "CC")

  `customAnnot` - Use if `mapping` argument is set to "custom". It can be an object generated by `GAFReader` or `readGAF` function from mgsa package or list which has GO term ids as keys and character vectors contain gene ids as values.

  `annot` - from TopGO manual: These functions are used to compile a list of GO terms such that each element in the list is a character vector containing all the gene identifiers that are mapped to the respective GO term.

  `bggenes` - vector contains background set of genes

  ... - other parameters:

  `genesannot` - minimal number of genes annotated to a term in the annotation. 1 by default

  `algorithm` - from TopGO manual: character string specifing which algorithm to use. The algorithms are shown by the topGO whichAlgorithms() function. "classic" by default

  `statistic` - from TopGO manual: character string specifing which test to use. The statistical tests are shown by the topGO whichTests() function. "fisher" by default

  `mapping` - from TopGO manual: character string specifieng the name of the Bioconductor package containing the gene mappings for a specific organism. For example: mapping = "org.Hs.eg.db". "custom" by default

  `ID` - from TopGO manual: character string specifing the gene identifier to use. Currently only the following identifiers can be used: c("entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene")

### Accessors

In the code examples below `object` is an object of FuncAnnotGroupsTopGO class

  `getResultList(object)` - returns list of functional annotation result tables

### Examples

    # read .gaf file (in this example gaf file with annotation for \emph{A.thaliana} is used)
    library(topGO)
    gaf_path <- system.file("extdata", "gene_association.tair.lzma",
                             package = "FoldGO", mustWork = TRUE)
    # read gaf file and convert annoitation in the list format
    # contains GO term id's as keys and Gene ID's as values
    gaf <- GAFReader(file = gaf_path, geneid_col = 10)
    # split DEG genes into quantiles
    gene_groups <- GeneGroups(degenes, 2)
    # run enrichment test
    annotobj <- FuncAnnotGroupsTopGO(gene_groups,"BP", customAnnot = gaf,
                                     annot = topGO::annFUN.GO2genes,
                                     bggenes = bggenes, padjmethod = "BH",
                                     qitborder = 10, genesannot = 1)

    # get results of functional enrichment analysis in a tabular form:
    getResultList(annotobj)

[Package FoldGO version 1.2.3 Index]