calculateCPM {scater}R Documentation

Calculate counts per million (CPM)

Description

Calculate count-per-million (CPM) values from the count data.

Usage

calculateCPM(object, exprs_values = "counts", use_size_factors = TRUE,
  subset_row = NULL)

Arguments

object

A SingleCellExperiment object or count matrix.

exprs_values

A string specifying the assay of object containing the count matrix, if object is a SingleCellExperiment.

use_size_factors

A logical scalar indicating whether size factors in object should be used to compute effective library sizes. If not, all size factors are deleted and library size-based factors are used instead (see librarySizeFactors. Alternatively, a numeric vector containing a size factor for each cell, which is used in place of sizeFactor(object).

subset_row

A vector specifying the subset of rows of object for which to return a result.

Details

If requested, size factors are used to define the effective library sizes. This is done by scaling all size factors such that the mean scaled size factor is equal to the mean sum of counts across all features. The effective library sizes are then used to in the denominator of the CPM calculation.

Assuming that object is a SingleCellExperiment:

If no size factors are available, the library sizes will be used.

If object is a matrix or matrix-like object, size factors will only be used if use_size_factors is a numeric vector. Otherwise, the sum of counts for each cell is directly used as the library size.

Value

Numeric matrix of CPM values.

Examples

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

cpm(example_sce) <- calculateCPM(example_sce, use_size_factors = FALSE)


[Package scater version 1.10.1 Index]