rnalysis.enrichment.RankedSet

class rnalysis.enrichment.RankedSet(ranked_genes: Union[Filter, List[str], Tuple[str], ndarray], set_name: str = '')

Receives a ranked gene set, sorted by any biologically-meaningful value (expression level, fold-change, etc) and preforms various enrichment analyses on them. ALl functions that can be applied to FeatureSet objects can also be applied to RankedSet objects.

__init__(ranked_genes: Union[Filter, List[str], Tuple[str], ndarray], set_name: str = '')

Parameters

gene_set (filtering.Filter object, set of strings or list of strings) – the set of genomic features to be used in downstream analyses
set_name (str) – name of the FeatureSet

Examples

>>> from rnalysis import enrichment, filtering
>>> my_set = enrichment.FeatureSet({'gene1','gene2','gene2'}, 'name of my set')

>>> filter_obj = filtering.CountFilter('tests/test_files/counted.csv')
>>> my_other_set = enrichment.FeatureSet(filter_obj, 'name of my other set')

`RankedSet.add`	Add an element to a set.
`RankedSet.biotypes_from_gtf`(gtf_path[, ...])	Returns a DataFrame describing the biotypes in the table and their count.
`RankedSet.biotypes_from_ref_table`([ref])	Returns a DataFrame describing the biotypes in the gene set and their count.
`RankedSet.change_set_name`(new_name)	Change the 'set_name' of a FeatureSet to a new name.
`RankedSet.clear`	Remove all elements from this set.
`RankedSet.copy`	Return a shallow copy of a set.
`RankedSet.difference`(*others)	Calculates the set difference of the indices from multiple FeatureSet objects (the indices that appear in the first FeatureSet object but NOT in the other objects).
`RankedSet.difference_update`	Remove all elements of another set from this set.
`RankedSet.discard`	Remove an element from a set if it is a member.
`RankedSet.filter_biotype_from_gtf`(gtf_path)	Filters out all features that do not match the indicated biotype/biotypes (for example: 'protein_coding', 'ncRNA', etc).
`RankedSet.filter_biotype_from_ref_table`([...])	Filters out all features that do not match the indicated biotype/biotypes (for example: 'protein_coding', 'ncRNA', etc).
`RankedSet.filter_by_attribute`([attributes, ...])	Filters features according to user-defined attributes from an Attribute Reference Table.
`RankedSet.filter_by_go_annotations`(go_ids[, ...])	Filters genes according to GO annotations, keeping only genes that are annotated with a specific GO term.
`RankedSet.filter_by_kegg_annotations`(kegg_ids)	Filters genes according to KEGG pathways, keeping only genes that belong to specific KEGG pathway.
`RankedSet.find_paralogs_ensembl`([organism, ...])	Find paralogs within the same species using the Ensembl database.
`RankedSet.find_paralogs_panther`([organism, ...])	Find paralogs within the same species using the PantherDB database.
`RankedSet.go_enrichment`([organism, ...])	Calculates enrichment and depletion of the FeatureSet for Gene Ontology (GO) terms against a background set.
`RankedSet.intersection`(*others)	Calculates the set intersection of the indices from multiple FeatureSet objects (the indices that exist in ALL of the FeatureSet objects).
`RankedSet.intersection_update`	Update a set with the intersection of itself and another.
`RankedSet.isdisjoint`	Return True if two sets have a null intersection.
`RankedSet.issubset`	Report whether another set contains this set.
`RankedSet.issuperset`	Report whether this set contains another set.
`RankedSet.kegg_enrichment`([organism, ...])	Calculates enrichment and depletion of the FeatureSet for Kyoto Encyclopedia of Genes and Genomes (KEGG) curated pathways against a background set.
`RankedSet.map_orthologs_ensembl`(map_to_organism)	Map genes to their nearest orthologs in a different species using the Ensembl database.
`RankedSet.map_orthologs_orthoinspector`(...)	Map genes to their nearest orthologs in a different species using the OrthoInspector database.
`RankedSet.map_orthologs_panther`(map_to_organism)	Map genes to their nearest orthologs in a different species using the PantherDB database.
`RankedSet.map_orthologs_phylomedb`(...[, ...])	Map genes to their nearest orthologs in a different species using the PhylomeDB database. This function generates a table describing all matching discovered ortholog pairs (both unique and non-unique) and returns it, and can also translate the genes in this data table into their nearest ortholog, as well as remove unmapped genes.
`RankedSet.non_categorical_enrichment`([...])	Calculates enrichment and depletion of the FeatureSet for user-defined non-categorical attributes against a background set using either a one-sample T-test or Sign test.
`RankedSet.pop`	Remove and return an arbitrary set element.
`RankedSet.remove`	Remove an element from a set; it must be a member.
`RankedSet.save_txt`(fname)	Save the list of features in the FeatureSet object under the specified filename and path.
`RankedSet.single_set_enrichment`(attributes)	Calculates enrichment and depletion of the sorted RankedSet for user-defined attributes WITHOUT a background set, using the generalized Minimum Hypergeometric Test (XL-mHG, developed by `Prof.
`RankedSet.single_set_go_enrichment`([...])	Calculates enrichment and depletion of the sorted RankedSet for Gene Ontology (GO) terms WITHOUT a background set, using the generalized Minimum Hypergeometric Test (XL-mHG, developed by `Prof.
`RankedSet.single_set_kegg_enrichment`([...])	Calculates enrichment and depletion of the sorted RankedSet for Kyoto Encyclopedia of Genes and Genomes (KEGG) curated pathways WITHOUT a background set, using the generalized Minimum Hypergeometric Test (XL-mHG, developed by `Prof.
`RankedSet.symmetric_difference`(other)	Calculates the set symmetric difference of the indices from two FeatureSet objects (the indices that appear in EXACTLY ONE of the FeatureSet objects, and not both/neither).
`RankedSet.symmetric_difference_update`	Update a set with the symmetric difference of itself and another.
`RankedSet.translate_gene_ids`(translate_to[, ...])	Translates gene names/IDs from one type to another.
`RankedSet.union`(*others)	Calculates the set union of the indices from multiple FeatureSet objects (the indices that exist in at least one of the FeatureSet objects).
`RankedSet.update`	Update a set with the union of itself and others.
`RankedSet.user_defined_enrichment`(attributes)	Calculates enrichment and depletion of the FeatureSet for user-defined attributes against a background set.