R Interface with InterMine-Powered Databases

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Documentation for package ‘InterMineR’ version 1.22.0

• 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
create_list	Methods for managing and doing operations with 'ListManager-class' objects.
create_list-method	Methods for managing and doing operations with 'ListManager-class' objects.
create_list-methods	Methods for managing and doing operations with 'ListManager-class' objects.
delete_lists	Methods for managing and doing operations with 'ListManager-class' objects.
delete_lists-method	Methods for managing and doing operations with 'ListManager-class' objects.
delete_lists-methods	Methods for managing and doing operations with 'ListManager-class' objects.
difference	Methods for managing and doing operations with 'ListManager-class' objects.
difference-method	Methods for managing and doing operations with 'ListManager-class' objects.
difference-methods	Methods for managing and doing operations with 'ListManager-class' objects.
doEnrichment	Perform enrichment analysis
doEnrichment,webservice-methods	Perform enrichment analysis
doEnrichment-methods	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
get_list	Methods for managing and doing operations with 'ListManager-class' objects.
get_list-method	Methods for managing and doing operations with 'ListManager-class' objects.
get_list-methods	Methods for managing and doing operations with 'ListManager-class' objects.
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.
intersect	Methods for managing and doing operations with 'ListManager-class' objects.
intersect-method	Methods for managing and doing operations with 'ListManager-class' objects.
intersect-methods	Methods for managing and doing operations with 'ListManager-class' objects.
listDatasets	Retrieve all types of InterMine features that possess dataSets as a child_name.
ListManager-class	ListManager class provides methods to manage list contents and operations.
ListManager-methods	Methods for managing and doing operations with 'ListManager-class' objects.
listMines	List the available InterMine-powered databases
list_manager	A Class for Managing List Content and Operations
list_manager,webservice-methods	A Class for Managing List Content and Operations
list_manager-methods	A Class for Managing List Content and Operations
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
subtract	Methods for managing and doing operations with 'ListManager-class' objects.
subtract-method	Methods for managing and doing operations with 'ListManager-class' objects.
subtract-methods	Methods for managing and doing operations with 'ListManager-class' objects.
summary	Summarize InterMineR query constraints
summary-method	Summarize InterMineR query constraints
union	Methods for managing and doing operations with 'ListManager-class' objects.
union-method	Methods for managing and doing operations with 'ListManager-class' objects.
union-methods	Methods for managing and doing operations with 'ListManager-class' objects.
webservice-class	Service class represents connections to different InterMine WebServices
webservice-methods	Perform enrichment analysis
webservice-methods	A Class for Managing List Content and Operations