sumCountsAcrossCells {scater}R Documentation

Sum counts across a set of cells

Description

Create a count matrix where counts for all cells in a set are summed together.

Usage

sumCountsAcrossCells(object, ids, exprs_values = "counts",
  BPPARAM = SerialParam())

Arguments

object

A SingleCellExperiment object or a count matrix.

ids

A factor specifying the set to which each cell in object belongs.

exprs_values

A string or integer scalar specifying the assay of object containing counts, if object is a SingleCellExperiment.

BPPARAM

A BiocParallelParam object specifying how summation should be parallelized.

Details

This function provides a convenient method for aggregating counts across multiple columns for each feature. A typical application would be to sum counts across all cells in each cluster to obtain “pseudo-bulk” samples for further analysis.

Any NA values in ids are implicitly ignored and will not be considered or reported. This may be useful, e.g., to remove undesirable cells by setting their entries in ids to NA.

Value

A count matrix where counts for all cells in the same set are summed together for each feature.

Author(s)

Aaron Lun

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sce <- SingleCellExperiment(
    assays = list(counts = sc_example_counts), 
    colData = sc_example_cell_info)

ids <- sample(LETTERS[1:5], ncol(example_sce), replace=TRUE)
out <- sumCountsAcrossCells(example_sce, ids)
dimnames(out)

[Package scater version 1.12.2 Index]