subjectMetaData: Collate metadata variation

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

Description

Identify single cell experiment metadata variables that are identical within subject (e.g. genotype, treatment, cell line, sample preparation). Effectively excludes metadata variables containing between cell variation. Used as the design matrix for differential expression analysis.

Usage

subjectMetaData(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

Tibble data frame of metadata variables without intrasubject variation from single cell experiment metadata. Rows correspond to aggregated cells (i.e. subject / biological replicate) and columns to metadata attribute variables (e.g. genotype, treatment, cell line).

Examples

## Return experiment metadata sans intrasubject variation.
subjectMetaData(scExp=small_airway, subjectVar="orig.ident")

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