countsByCell {aggregateBioVar} | R Documentation

## Within cell type gene-by-subject matrices

### Description

Given a vector of unique cell types, calculate a gene-by-subject matrix and inter-subject metadata for a differential expression design matrix.

### Usage

    countsByCell(scExp, subjectVar, cellVar)

### Arguments

`scExp` | SingleCellExperiment object containing (at minimum) gene counts and column metadata describing sample identifiers and cell types.
`subjectVar` | Metadata column name assigning biological sample identity to aggregate within-subject feature counts.
`cellVar` | Metadata column name assigning cell type. Used for aggregating gene-by-subject count matrices by cell type.

### Value

List of gene-by-subject and design matrices for each cell type.

### See Also

`summarizedCounts` for aggregate counts and metadata SummarizedExperiment object.

### Examples

    ## Return list of `SummarizedExperiments` with gene-by-subject count matrices
    ## and subject metadata for each unique `SingleCellExperiment` cell type.
    countsByCell(
        scExp=small_airway,
        subjectVar="orig.ident", cellVar="celltype"
    )

[Package aggregateBioVar version 1.0.0 Index]