common_classes: list and count samples with common ontological annotation in...

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

list and count samples with common ontological annotation in two SEs

Description

list and count samples with common ontological annotation in two SEs

Usage

common_classes(ont, se1, se2)

Arguments

ont	instance of ontologyIndex ontology
se1	a SummarizedExperiment using 'label.ont' in colData to provide ontological tags (from 'ont') for samples
se2	a SummarizedExperiment using 'label.ont' in colData to provide ontological tags (from 'ont') for samples

Value

a data.frame with rownames given by the common tags, the class names as column 'clname', and counts of samples bearing the given tags in remaining columns.

Examples

if (requireNamespace("celldex")) {
  imm = celldex::ImmGenData()
  if ("label.ont" %in% names(SummarizedExperiment::colData(imm))) {
    cl = getOnto("cellOnto")
    blu = celldex::BlueprintEncodeData()
    common_classes( cl, imm, blu )
    }
  }

vjcitn/ontoProc documentation built on Nov. 27, 2024, 4:38 p.m.