calculateCPM {scater} | R Documentation

## Calculate counts per million (CPM)

### Description

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

### Usage

    calculateCPM(object, use.size.factors = TRUE)

### Arguments

`object` | an `SingleCellExperiment` object
`use.size.factors` | a logical scalar specifying whether the size factors should be used to construct effective library sizes, or if the library size should be directly defined as the sum of counts for each cell.

### Value

Matrix of CPM values.

### Examples

    data("sc_example_counts")
    data("sc_example_cell_info")
    example_sce <- SingleCellExperiment(
    assays = list(counts = sc_example_counts), colData = sc_example_cell_info)
    cpm(example_sce) <- calculateCPM(example_sce, use.size.factors = FALSE)

[Package scater version 1.6.3 Index]