aggregateBioVar: Aggregate subject-level biological variation

In jasonratcliff/aggregateBioVar: Differential Gene Expression Analysis for Multi-subject scRNA-seq

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"
)

jasonratcliff/aggregateBioVar documentation built on Sept. 29, 2020, 11:53 p.m.