summarizedCounts: Aggregate feature counts and metadata by subject

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

Description

Given an input sparse count matrix and corresponding column metadata, aggregate gene counts by subject level. Metadata variables with only inter-subject variation are retained; any variables with cell-level variation within a subject are dropped (e.g. feature / RNA count by cell).

Usage

summarizedCounts(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

SummarizedExperiment object with feature counts aggregated by subject and summarized inter-subject metadata.

Examples

## Construct SummarizedExperiment object with gene-by-subject count matrix
## and column metadata summarized to exclude intrasubject variation.
## See `SummarizedExperiment` accessor functions `assay()` and `colData()`
## to access the count matrix and column metadata for downstream analyses.
summarizedCounts(scExp=small_airway, subjectVar="orig.ident")

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