subset_descendants: subset a SummarizedExperiment to which ontology tags have...

In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

subset a SummarizedExperiment to which ontology tags have been bound using 'bind_formal_tags', obtaining the 'descendants' of the class of interest

Description

subset a SummarizedExperiment to which ontology tags have been bound using 'bind_formal_tags', obtaining the 'descendants' of the class of interest

Usage

subset_descendants(
  se,
  onto,
  class_name,
  class_tag,
  formal_cd_name = "label.ont"
)

Arguments

se	SummarizedExperiment instance
onto	representation of an ontology using representation from ontologyIndex package
class_name	character(1) if 'class_tag' is missing, this will be grepped in onto[["name"]] to find class and its descendants
class_tag	character(1) used if given to identify "ontological descendants" of this term in se
formal_cd_name	character(1) tells name used for ontology tag column in 'colData(se)'

Value

instance of SummarizedExperiment

vjcitn/ontoProc documentation built on March 23, 2024, 7:23 a.m.