aggregateBioVar {aggregateBioVar} | R Documentation |
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.
aggregateBioVar(scExp, subjectVar, cellVar)
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. |
List of SummarizedExperiment objects with gene-by-subject count matrices and variable inter-subject column metadata across and within cell types.
## Aggregate gene-by-subject count matrix and inter-subject metadata aggregateBioVar( scExp=small_airway, subjectVar="orig.ident", cellVar="celltype" )