calcAverage {scater}R Documentation

Calculate average counts, adjusting for size factors or library size

Description

Calculate average counts per feature, adjusting them as appropriate to take into account for size factors for normalization or library sizes (total counts).

Usage

calcAverage(object, size.factors = NULL)

Arguments

object

a SingleCellExperiment object or a matrix of counts

size.factors

numeric(), vector of size factors to use to scale library size in computation of counts-per-million. Extracted from the object if it is a SingleCellExperiment object; if object is a matrix, then if non-NULL, the provided size factors are used. Default is NULL, in which case size factors are all set to 1 (i.e. library size adjustment only).

Value

Vector of average count values with same length as number of features.

Examples

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

## calculate average counts
ave_counts <- calcAverage(example_sce)
[Package scater version 1.6.3 Index]