aggregateBioVar {aggregateBioVar} | R Documentation

## Aggregate subject-level biological variation

### Description

Given an input gene-by-cell count matrix from a SingleCellExperiment object, sum within-subject gene counts into an aggregate gene-by-subject count matrix. Column metadata accessed by colData are collated by subjectMetaData to remove variables with inter-cell intrasubject variation, effectively retaining between-subject variation. The summary operations are performed across all cell types and within each cell type. A list of SummarizedExperiment objects is returned each with aggregate gene-by-subject count matrix and inter-subject metadata.

### Usage

    aggregateBioVar(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 SummarizedExperiment objects with gene-by-subject count matrices and variable inter-subject column metadata across and within cell types.

### Examples

    ## Aggregate gene-by-subject count matrix and inter-subject metadata
    aggregateBioVar(
        scExp=small_airway,
        subjectVar="orig.ident", cellVar="celltype"
    )

[Package aggregateBioVar version 1.0.0 Index]