librarySizeFactors {scater}R Documentation

Compute library size factors

Description

Define per-cell size factors from the library sizes (i.e., total sum of counts per cell).

Usage

librarySizeFactors(x, ...)

## S4 method for signature 'ANY'
librarySizeFactors(x, subset_row = NULL)

## S4 method for signature 'SummarizedExperiment'
librarySizeFactors(x,
  exprs_values = "counts", ...)

computeLibraryFactors(x, ..., altexp = NULL)

Arguments

x

For libarySizeFactors, a numeric matrix of counts with one row per feature and column per cell. Alternatively, a SummarizedExperiment or SingleCellExperiment containing such counts.

For computeLibraryFactors, only a SingleCellExperiment is accepted.

...

For the librarySizeFactors generic, arguments to pass to specific methods. For the SummarizedExperiment method, further arguments to pass to the ANY method.

For computeLibraryFactors, further arguments to pass to librarySizeFactors.

subset_row

A vector specifying whether the size factors should be computed from a subset of rows of x.

exprs_values

String or integer scalar indicating the assay of x containing the counts.

altexp

String or integer scalar indicating which (if any) alternative experiment should be used to provide the counts to compute the size factors.

Details

Library sizes are converted into size factors by scaling them so that their mean across cells is unity. This ensures that the normalized values are still on the same scale as the raw counts.

Preserving the scale is useful for interpretation of operations on the normalized values, e.g., the pseudo-count used in logNormCounts can actually be considered an additional read/UMI. This is important for ensuring that the effect of the pseudo-count decreases with increasing sequencing depth.

Setting altexp is occasionally useful for computing size factors from spike-in transcripts and using them on the count matrix for endogenous genes (stored in the main experiment).

Value

For librarySizeFactors, a numeric vector of size factors is returned for all methods.

For computeLibraryFactors, a numeric vector is also returned for the ANY and SummarizedExperiment methods. For the SingleCellExperiment method, x is returned containing the size factors in sizeFactors(x).

Author(s)

Aaron Lun

See Also

logNormCounts, where these size factors are used by default.

Examples

example_sce <- mockSCE()
summary(librarySizeFactors(example_sce))

[Package scater version 1.14.0 Index]