convertToGeneAnswers {InterMineR} | R Documentation

## Convert InterMineR enrichment analysis results to GeneAnswers object

### Description

`convertToGeneAnswers` constitutes a wrapper function for converting the results of `doEnrichment` function to a `GeneAnswers-class` object. This way the user can utilize the functions of `GeneAnswers` package to visualize the results of InterMineR enrichment analysis.

### Usage

    convertToGeneAnswers(
      enrichmentResult,
      geneInput,
      geneInputType,
      geneExprProfile,
      annLib,
      categoryType,
      enrichCategoryChildName
    )

### Arguments

`enrichmentResult` | a list containing the results of `doEnrichment` function.
`geneInput` | a data.frame containing the gene identifiers used for the InterMineR enrichment analysis, and possible values associated with them.
`geneInputType` | a character string specifying the InterMineR gene identifier type of the values assigned to geneInput argument. InterMineR identifiers for each Mine can be retrieved with `getModel` function.
`geneExprProfile` | a data.frame containing gene expression information (optional)
`annLib` | name of given annotation library file or user provided annotation list.
`categoryType` | name of given annotation category or NULL for user provided annotation list.
`enrichCategoryChildName` | a character string specifying the InterMIneR annotation category identifier. This argument must be assigned manually if: 1) 'enrichIdentifier' column is missing from the widgets of the Mine used by `doEnrichment`, 2) the value of 'enrichIdentifier' for the enrichment widget used by `doEnrichment` is NA. InterMineR identifiers for each Mine can be retrieved with `getModel` function.

### Value

a `GeneAnswers-class` object.

### Author(s)

InterMine Team

### References

https://bioconductor.org/packages/release/bioc/html/GeneAnswers.html

### See Also

`doEnrichment`, `GeneAnswers-class`, `getWidgets`, `getModel`

### Examples

    # load human genes which are associated with Diabetes (retrieved from HumanMine)
    data("PL_DiabetesGenes")

    # get Gene.primaryIdentifiers (ENTREZ Gene identifier)
    hsa_gene_entrez = as.character(PL_DiabetesGenes$Gene.primaryIdentifier)

    # perform enrichment analysis with InterMineR
    hsa_enrichResult = doEnrichment(
      im = initInterMine(listMines()["HumanMine"]),
      genelist = "PL_DiabetesGenes",
      widget = "go_enrichment_for_gene",
      correction = "Benjamini Hochberg"
    )

    # convert InterMineR enrichment analysis results to a GeneAnswers object
    # Do not run unless you have installed and loaded GeneAnswers package!

    # load GeneAnswers
    library(GeneAnswers)

    hsa_geneanswers = convertToGeneAnswers(
      enrichmentResult = hsa_enrichResult,
      geneInput = data.frame(GeneID = as.character(hsa_gene_entrez),
                             stringsAsFactors = FALSE),
      geneInputType = "Gene.primaryIdentifier",
      annLib = 'org.Hs.eg.db',
      categoryType = "GO"
      # enrichCategoryChildName = "Gene.goAnnotation.ontologyTerm.parents.identifier"
    )

[Package InterMineR version 1.4.1 Index]