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build_query()
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Process a GraphQL query from COMPASS API |
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create_module()
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create a module providing both biological features and sample sets |
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create_module_bf()
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create a module based on provided biological features |
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create_module_ss()
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create a module based on provided sample sets |
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describe_module()
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describe a module |
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enrich_module()
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show the enrichment for ontology terms for both sampleSets and biofeatures |
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get_OntologyNode()
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get_OntologyNode |
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get_annotation_triples()
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get_annotation_triples |
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get_available_compendia()
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Get all available compendia in COMPASS |
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get_available_normalization()
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get_available_normalization |
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get_available_plot_methods()
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show all available plot methods |
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get_biofeature_annotations()
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get_biofeature_annotations |
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get_biofeature_by_name()
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get_biofeature_by_name |
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get_biofeature_id()
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get_biofeature_id |
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get_biofeature_ranking()
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get_biofeature_ranking() |
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get_compass_version()
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get the current version of COMPASS |
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get_compendium_data_source()
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Get compendium data sources |
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get_experimentId_by_sampleSetId()
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Get experimentAccessid and experimentName from sampleName |
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get_experiments()
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Get experimentAccessid and experimentName from sampleName |
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get_ids_from_alias()
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get_ids_from_alias |
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get_ontologies()
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Get all available ontologies for the selected compendium |
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get_ontology_structure()
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get_ontology_structure |
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get_platform_information()
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Get information about all available platforms for the selected compendium,
use get_available_compendia to check all the available compendia |
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get_ranking()
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get_ranking |
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get_raw_data()
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get raw data for a particular sample |
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get_sample_annotation()
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get annotations for either n samples or selected sampleName |
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get_sample_by_gsm()
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retrieve internal id, name (GSM), description for sample providing sampleName (GSM) |
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get_samples()
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Get all samples measured with a given platform |
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get_samples_by_gse()
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retrieve internal id, name (GSM), description from all samples with experiment id (GSE) |
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get_samples_by_sampleSet()
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Get all samples id for a selected sampleSet |
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get_samples_info()
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get_samples_info |
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get_sampleset_by_sampleid()
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get_sampleset_by_sampleid |
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get_sampleset_id()
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get_sampleset_id |
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get_samplesets_ranking()
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get_samplesets_ranking |
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get_sparql_annotation_triples()
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get_sparql_annotation_triples |
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plot_annotation_network()
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plot rdf network |
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plot_module_distribution()
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Plot a distribution from a model |
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plot_module_heatmap()
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plot heatmap from a module |
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plot_module_network()
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Plot a network from a model |
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rcompass-package
|
COMPASS (COMpendia Programmatic Access Support Software) API client library |
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totalCounts()
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totalCounts for aggregated types |
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view_plot()
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Show a plot using the rstudio viewer |