countsByCell: Within cell type gene-by-subject matrices

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

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"
)

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