areSizeFactorsCentred {scater} | R Documentation

## Check if the size factors are centred at unity

### Description

Checks if each set of size factors is centred at unity, such that abundances can be reasonably compared between features normalized with different sets of size factors.

### Usage

    areSizeFactorsCentred(object, centre = 1, tol = 1e-06)

### Arguments

`object` | an `SingleCellExperiment` object containing multiple sets of size factors.
`centre` | a numeric scalar, the value around which all sets of size factors should be centred.
`tol` | a numeric scalar, the tolerance for testing equality of the mean of each size factor set to `centre`.

### Value

a `SingleCellExperiment` object with centred size factors

### Examples

    data("sc_example_counts")
    data("sc_example_cell_info")
    example_sce <- SingleCellExperiment(
    assays = list(counts = sc_example_counts), colData = sc_example_cell_info)
    keep_gene <- rowSums(counts(example_sce)) > 0
    example_sce <- example_sce[keep_gene,]

    sizeFactors(example_sce) <- runif(ncol(example_sce))
    areSizeFactorsCentred(example_sce)
    example_sce <- normalize(example_sce, centre = TRUE)
    areSizeFactorsCentred(example_sce)

[Package scater version 1.6.3 Index]