rnalysis.filtering.CountFilter.filter_by_go_annotations

CountFilter.filter_by_go_annotations(go_ids: str | List[str], mode: Literal['union', 'intersection'] = 'union', organism: str | int | Literal['auto'] | Literal['Arabodopsis thaliana', 'Caenorhabditis elegans', 'Danio rerio', 'Drosophila melanogaster', 'Escherichia coli', 'Homo sapiens', 'Mus musculus', 'Saccharomyces cerevisiae', 'Schizosaccharomyces pombe'] = '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', propagate_annotations: bool = True, evidence_types: Literal['any', 'experimental', 'phylogenetic', 'computational', 'author', 'curator', 'electronic'] | Iterable[Literal['experimental', 'phylogenetic', 'computational', 'author', 'curator', 'electronic']] = 'any', excluded_evidence_types: Literal['experimental', 'phylogenetic', 'computational', 'author', 'curator', 'electronic'] | Iterable[Literal['experimental', 'phylogenetic', 'computational', 'author', 'curator', 'electronic']] = (), databases: str | Iterable[str] = 'any', excluded_databases: str | Iterable[str] = (), qualifiers: Literal['any', 'not', 'contributes_to', 'colocalizes_with'] | Iterable[Literal['not', 'contributes_to', 'colocalizes_with']] = 'any', excluded_qualifiers: Literal['not', 'contributes_to', 'colocalizes_with'] | Iterable[Literal['not', 'contributes_to', 'colocalizes_with']] = 'not', opposite: bool = False, inplace: bool = True)

Filters genes according to GO annotations, keeping only genes that are annotated with a specific GO term. When multiple GO terms are given, filtering can be done in ‘union’ mode (where genes that belong to at least one GO term are not filtered out), or in ‘intersection’ mode (where only genes that belong to ALL GO terms are not filtered out).

Parameters:

  • go_ids (str or list of str)

  • mode ('union' or 'intersection'.) – If ‘union’, filters out every genomic feature that does not belong to one or more of the indicated attributes. If ‘intersection’, filters out every genomic feature that does not belong to ALL of the indicated attributes.

param organism: organism name or NCBI taxon ID for which the function will fetch GO annotations. :type 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 propagate_annotations: determines the propagation method of GO annotations. ‘no’ does not propagate annotations at all; ‘classic’ propagates all annotations up to the DAG tree’s root; ‘elim’ terminates propagation at nodes which show significant enrichment; ‘weight’ performs propagation in a weighted manner based on the significance of children nodes relatively to their parents; and ‘allm’ uses a combination of all proopagation methods. To read more about the propagation methods, see Alexa et al: https://pubmed.ncbi.nlm.nih.gov/16606683/ :type propagate_annotations: ‘classic’, ‘elim’, ‘weight’, ‘all.m’, or ‘no’ (default=’elim’) :param evidence_types: only annotations with the specified evidence types will be included in the analysis. For a full list of legal evidence codes and evidence code categories see the GO Consortium website: http://geneontology.org/docs/guide-go-evidence-codes/ :type evidence_types: str, Iterable of str, ‘experimental’, ‘phylogenetic’ ,’computational’, ‘author’, ‘curator’, ‘electronic’, or ‘any’ (default=’any’) :param excluded_evidence_types: annotations with the specified evidence types will be excluded from the analysis. For a full list of legal evidence codes and evidence code categories see the GO Consortium website: http://geneontology.org/docs/guide-go-evidence-codes/ :type excluded_evidence_types: str, Iterable of str, ‘experimental’, ‘phylogenetic’ ,’computational’, ‘author’, ‘curator’, ‘electronic’, or None (default=None) :param databases: only annotations from the specified databases will be included in the analysis. For a full list of legal databases see the GO Consortium website: http://amigo.geneontology.org/xrefs :type databases: str, Iterable of str, or ‘any’ (default) :param excluded_databases: annotations from the specified databases will be excluded from the analysis. For a full list of legal databases see the GO Consortium website: http://amigo.geneontology.org/xrefs :type excluded_databases: str, Iterable of str, or None (default) :param qualifiers: only annotations with the speficied qualifiers will be included in the analysis. Legal qualifiers are ‘not’, ‘contributes_to’, and/or ‘colocalizes_with’. :type qualifiers: str, Iterable of str, or ‘any’ (default) :param excluded_qualifiers: annotations with the speficied qualifiers will be excluded from the analysis. Legal qualifiers are ‘not’, ‘contributes_to’, and/or ‘colocalizes_with’. :type excluded_qualifiers: str, Iterable of str, or None (default=’not’) :type opposite: bool (default=False) :param opposite: If True, the output of the filtering will be the OPPOSITE of the specified (instead of filtering out X, the function will filter out anything BUT X). If False (default), the function will filter as expected. :type inplace: bool (default=True) :param inplace: If True (default), filtering will be applied to the current FeatureSet object. If False, the function will return a new FeatureSet instance and the current instance will not be affected. :return: If ‘inplace’ is False, returns a new, filtered instance of the FeatureSet object.