# R Interface with InterMine-Powered Databases

## Documentation for package ‘InterMineR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

InterMineR-package | R Interface with InterMine-powered databases
convertToGeneAnswers | Convert InterMineR enrichment analysis results to GeneAnswers object
convertToGRanges | Convert InterMineR retrieved genomic information to objects of class 'GRanges'
convertToRangedSummarizedExperiment | Convert experimental results retrieved by InterMineR queries to an object of the 'RangedSummarizedExperiment' class
doEnrichment | Perform enrichment analysis
getDatasets | Retrieve information about the available datasets of a Mine instance.
getDescription | Methods for accessing 'InterMineR-class' objects.
getDescription-method | Methods for accessing 'InterMineR-class' objects.
getDescription-methods | Methods for accessing 'InterMineR-class' objects.
getGeneIds | Get Gene.id values for a list of gene identifiers
getModel | Get the model of InterMine
getName | Methods for accessing 'InterMineR-class' objects.
getName-method | Methods for accessing 'InterMineR-class' objects.
getName-methods | Methods for accessing 'InterMineR-class' objects.
getOrderBy | Methods for accessing 'InterMineR-class' objects.
getOrderBy-method | Methods for accessing 'InterMineR-class' objects.
getOrderBy-methods | Methods for accessing 'InterMineR-class' objects.
getRelease | Get the current release information of InterMine
getSelect | Methods for accessing 'InterMineR-class' objects.
getSelect-method | Methods for accessing 'InterMineR-class' objects.
getSelect-methods | Methods for accessing 'InterMineR-class' objects.
getTemplateQuery | Get the query contained in a template
getTemplates | Get the information (name and title) of the templates pre-defined in InterMine
getVersion | Get the version information of InterMine
getWhere | Methods for accessing 'InterMineR-class' objects.
getWhere-method | Methods for accessing 'InterMineR-class' objects.
getWhere-methods | Methods for accessing 'InterMineR-class' objects.
getWidgets | Get the widgets of InterMine
initInterMine | Initialize the list containing the base URL and API token.
InterMineR | R Interface with InterMine-powered databases
InterMineR-class | InterMineR class contains the input values for performing queries in an InterMine instance.
InterMineR-methods | Methods for accessing 'InterMineR-class' objects.
listDatasets | Retrieve all types of InterMine features that possess dataSets as a child_name.
listMines | List the available InterMine-powered databases
newQuery | Initialize a new list query
PL_DiabetesGenes | PL_DiabetesGenes data
PL_FlyTF_site_specific_TFs | PL_FlyTF_site_specific_TFs data
runQuery | Run InterMineR queries
runQuery-method | Run InterMineR queries
setConstraints | setConstraints function is used to create a new or modify an existing list of constraints
setQuery | Initialize a new InterMineR query or modify an existing list query
simplifyResult | Convert multiple values of a column into Comma-separated character strings
summary | Summarize InterMineR query constraints
summary-method | Summarize InterMineR query constraints