rnalysis.filtering.Filter.map_orthologs_phylomedb

Filter.map_orthologs_phylomedb(map_to_organism: str | int | Literal, map_from_organism: Literal['auto'] | str | int | Literal = 'auto', gene_id_type: str | Literal['auto'] | Literal['UniProtKB AC/ID', 'UniParc', 'UniRef50', 'UniRef90', 'UniRef100', 'Gene Name', 'CRC64', 'Ensembl', 'Ensembl Genomes', 'Ensembl Genomes Protein', 'Ensembl Genomes Transcript', 'Ensembl Protein', 'Ensembl Transcript', 'GeneID', 'KEGG', 'PATRIC', 'UCSC', 'WBParaSite', 'WBParaSite Transcript/Protein', 'ArachnoServer', 'Araport', 'CGD', 'ConoServer', 'dictyBase', 'EchoBASE', 'euHCVdb', 'FlyBase', 'GeneCards', 'GeneReviews', 'HGNC', 'LegioList', 'Leproma', 'MaizeGDB', 'MGI', 'MIM', 'neXtProt', 'OpenTargets', 'Orphanet', 'PharmGKB', 'PomBase', 'PseudoCAP', 'RGD', 'SGD', 'TubercuList', 'VEuPathDB', 'VGNC', 'WormBase', 'WormBase Protein', 'WormBase Transcript', 'Xenbase', 'ZFIN', 'eggNOG', 'GeneTree', 'HOGENOM', 'OMA', 'OrthoDB', 'TreeFam', 'CCDS', 'EMBL/GenBank/DDBJ', 'EMBL/GenBank/DDBJ CDS', 'GI number', 'PIR', 'RefSeq Nucleotide', 'RefSeq Protein', 'ChiTaRS', 'GeneWiki', 'GenomeRNAi', 'PHI-base', 'CollecTF', 'BioCyc', 'PlantReactome', 'Reactome', 'UniPathway', 'CPTAC', 'ProteomicsDB'] = 'auto', consistency_score_threshold: Fraction = 0.5, filter_consistency_score: bool = True, non_unique_mode: Literal['first', 'last', 'random', 'none'] = 'first', remove_unmapped_genes: bool = False, inplace: bool = True)

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.

param map_to_organism:

organism name or NCBI taxon ID of the target species for ortholog mapping.

type map_to_organism:

str or int

param map_from_organism:

organism name or NCBI taxon ID of the input genes’ source species.

type map_from_organism:

str or int

param gene_id_type:

the identifier type of the genes/features in the FeatureSet object (for example: ‘UniProtKB’, ‘WormBase’, ‘RNACentral’, ‘Entrez Gene ID’). If the annotations fetched from the KEGG server do not match your gene_id_type, RNAlysis will attempt to map the annotations’ gene IDs to your identifier type. For a full list of legal ‘gene_id_type’ names, see the UniProt website: https://www.uniprot.org/help/api_idmapping

type gene_id_type:

str or ‘auto’ (default=’auto’)

` :param consistency_score_threshold: the minimum consistency score required for an ortholog mapping to be considered valid. Consistency scores are calculated by PhylomeDB and represent the confidence of the ortholog mapping. setting consistency_score_threshold to 0 will keep all mappings. You can read more about PhylomeDB consistency score on the PhylomeDB website: orthology.phylomedb.org/help

type consistency_score_threshold:: float between 0 and 1 (default=0.5)
param filter_consistency_score:: if True (default), when encountering non-unique ortholog mappings, RNAlysis will only keep the mappings with the highest consistency score.
type filter_consistency_score:: bool (default=True)
param non_unique_mode:: How to handle non-unique mappings. ‘first’ will keep the first mapping found for each gene; ‘last’ will keep the last; ‘random’ will keep a random mapping; and ‘none’ will discard all non-unique mappings.
type non_unique_mode:: ‘first’, ‘last’, ‘random’, or ‘none’ (default=’first’)
param remove_unmapped_genes:: if True, rows with gene names/IDs that could not be mapped to an ortholog will be dropped from the table. Otherwise, they will remain in the table with their original gene name/ID.
type remove_unmapped_genes:: bool (default=False)
type inplace:: bool (default=True)
param inplace:: If True (default), filtering will be applied to the current Filter object. If False, the function will return a new Filter instance and the current instance will not be affected.
return:: DataFrame describing all discovered mappings (unique and otherwise). If inplace=True, returns a filtered instance of the Filter object as well.