convertToGeneAnswers: Convert InterMineR enrichment analysis results to GeneAnswers...
In InterMineR: R Interface with InterMine-Powered Databases

Description Usage Arguments Value Author(s) References See Also Examples

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.

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

`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.

a GeneAnswers-class object.

InterMine Team

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

doEnrichment, GeneAnswers-class, getWidgets, getModel

# 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"
)