R Interface with InterMine-Powered Databases


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Documentation for package ‘InterMineR’ version 1.8.1

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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