countsBySubject: Gene-by-subject count matrix

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

Description

Convert gene-by-cell count matrix to gene-by-subject count matrix. Row sums are calculated for each feature (i.e. gene) across cells by subject.

Usage

countsBySubject(scExp, subjectVar)

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.

Value

S4 DataFrame of gene-by-subject count sums.

See Also

scSubjects for subjects values.

Examples

## Return cell count matrix aggregated by subject.
countsBySubject(scExp=small_airway, subjectVar="orig.ident")

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