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]