Gene Expression Atlas query and gene set enrichment package.


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Documentation for package ‘AtlasRDF’ version 1.10.0

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AtlasRDF-package Gene Expression Atlas query and gene set enrichment package.
AtlasRDF Gene Expression Atlas query and gene set enrichment package.
class:enrichmentresult Class '"enrichmentresult"'
class:factorbackground Class '"factorbackground"'
class:generef Class '"generef"'
class:pathwayresult Class '"pathwayresult"'
doFishersEnrichment Perform a gene set enrichment using gene list based on gene URIs.
doFishersEnrichmentForEnsemblIds Perform a gene set enrichment using gene list based on common ENSEMBL gene IDs.
doFishersEnrichmentForGeneNames Perform a gene set enrichment using gene list based on common gene names.
drawHeatMapForAtlasExperiment Produce a heatmap of differentially expressed genes vs conditions for an Atlas experiment.
enrichmentresult Class '"enrichmentresult"'
enrichmentresult-class Class '"enrichmentresult"'
excludeSubclasses Exclude subclasses of factors from enrichment results
factorbackground Class '"factorbackground"'
factorbackground-class Class '"factorbackground"'
generef Class '"generef"'
generef-class Class '"generef"'
getAllEnsemblGenesForExFactor Get all ENSEMBL genes reported as differentially expressed for a given experimental factor.
getExFactorURIFromLabel Get the EFO URI from a given label
getExperimentIdsForGeneURI Get ArrayExpress experiment ID which contain a gene specified by URI.
getExperimentsByDescription Search for experiments in Atlas based on a string, e.g. liver, cancer etc.
getExperimentURIsForGeneId Get experiment URIs which contain a gene specified by ENSEMBL ID.
getGeneListFromPubmedid Get gene lists in Atlas for a given pubmed id (assuming the data is in Atlas)
getGenesForExperimentID Get all of the genes reported in an experiment, speicifed by the Atlas experiment ID.
getGenesForExperimentURI Get all of the genes reported in an experiment, speicifed by the Atlas experiment URI.
getGenesForPathwayURI Get genes associated with a signalling pathway from Reactome.
getGeneUriFromEnsemblId Get gene URI from an ENSEMBL ID.
getGeneUriFromName Get URI of a gene based on the common gene name.
getLabel Get label of an entity based on the URI.
getOntologyMappings Get mappings for a given ontology class URI to EFO using the NCBO BioPortal
getPathwayForGeneId Get pathways associated to a gene.
getPathwaysFromGenesAndCondition Get pathways connected to genes which are differentially expressed for a user specified condition.
getPathwayUriFromName Get pathway URI given a pathway name
getRankedPathwaysForGeneIds Get pathway names and URIs for given gene list, sorted into list with most common pathways first.
getSpeciesSpecificEnsemblGenesForExFactor Get ENSEMBL genes which have been differentially expressed for a given condition and species.
getTaxonURI Get URI of a taxon class based on the common or taxonomic name.
includeOnlySubclasses Filter enrichment results to only include experimental factors of a given parent class (e.g. all cancers)
orderEnrichmentResults Order the results of a gene set enrichment by p-value.
pathwayresult Class '"pathwayresult"'
pathwayresult-class Class '"pathwayresult"'
searchForEFOTerms Search for EFO URIs from a given label text
transcription_pathway_enrichment Expression Gene Set Enrichment result for
vizPvalues Visualize the results of an enrichment filtering for a specificed p-value.