common_classes {ontoProc}R Documentation

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(colData(imm))) {
    cl = getCellOnto()
    blu = celldex::BlueprintEncodeData()
    common_classes( cl, imm, blu )
    }
  }

[Package ontoProc version 1.12.0 Index]