logNormCounts: Compute log-normalized expression values

In LTLA/scuttle: Single-Cell RNA-Seq Analysis Utilities

Compute log-normalized expression values

Description

Compute log-transformed normalized expression values from a count matrix in a SingleCellExperiment object.

Usage

logNormCounts(x, ...)

## S4 method for signature 'SummarizedExperiment'
logNormCounts(
  x,
  size.factors = NULL,
  log = NULL,
  transform = c("log", "none", "asinh"),
  pseudo.count = 1,
  center.size.factors = TRUE,
  ...,
  subset.row = NULL,
  normalize.all = FALSE,
  assay.type = "counts",
  name = NULL,
  BPPARAM = SerialParam(),
  size_factors = NULL,
  pseudo_count = NULL,
  center_size_factors = NULL,
  exprs_values = NULL
)

## S4 method for signature 'SingleCellExperiment'
logNormCounts(
  x,
  size.factors = sizeFactors(x),
  log = NULL,
  transform = c("log", "none", "asinh"),
  pseudo.count = 1,
  center.size.factors = TRUE,
  ...,
  subset.row = NULL,
  normalize.all = FALSE,
  assay.type = "counts",
  use.altexps = FALSE,
  name = NULL,
  BPPARAM = SerialParam(),
  size_factors = NULL,
  pseudo_count = NULL,
  center_size_factors = NULL,
  exprs_values = NULL,
  use_altexps = NULL
)

Arguments

x	A SingleCellExperiment or SummarizedExperiment object containing a count matrix.
...	For the generic, additional arguments passed to specific methods. For the methods, additional arguments passed to normalizeCounts.
size.factors	A numeric vector of cell-specific size factors. Alternatively NULL, in which case the size factors are computed from x.
log	Logical scalar indicating whether normalized values should be log2-transformed. This is retained for back-compatibility and will override any setting of transform. Users should generally use transform instead to specify the transformation.
transform	String specifying the transformation (if any) to apply to the normalized expression values.
pseudo.count	Numeric scalar specifying the pseudo-count to add when transform="log".
center.size.factors	Logical scalar indicating whether size factors should be centered at unity before being used.
subset.row	A vector specifying the subset of rows of x for which to return normalized values. If size.factors=NULL, the size factors are also computed from this subset.
normalize.all	Logical scalar indicating whether to return normalized values for all genes. If TRUE, any non-NULL value for subset.row is only used to compute the size factors. Ignored if subset.row=NULL or size.factors is supplied.
assay.type	A string or integer scalar specifying the assay of x containing the count matrix.
name	String containing an assay name for storing the output normalized values. Defaults to "logcounts" when transform="log", "ashcounts" when transform="asinh", and "normcounts" otherwise.
BPPARAM	A BiocParallelParam object specifying how library size factor calculations should be parallelized. Only used if size.factors is not specified.
size_factors, pseudo_count, center_size_factors, exprs_values	Deprecated.
use.altexps, use_altexps	Deprecated, use applySCE instead (see Examples).

Details

This function is a convenience wrapper around normalizeCounts. It returns a SingleCellExperiment or SummarizedExperiment containing the normalized values in a separate assay. This makes it easier to perform normalization by avoiding book-keeping errors during a long analysis workflow.

If NULL, size factors are determined as described in normalizeCounts. subset.row and normalize.all have the same interpretation as for normalizeCounts.

If x is a SingleCellExperiment, normalization is not applied to any alternative Experiments. Users can call applySCE to perform the normalization on each alternative Experiment - see Examples. Any Experiment-specific size factors will be automatically used, otherwise library size-based factors will be derived from the column sums.

Value

x is returned containing the (log-)normalized expression values in an additional assay named as name.

If x is a SingleCellExperiment, the size factors used for normalization are stored in sizeFactors. These are centered if center.size.factors=TRUE.

Author(s)

Aaron Lun, based on code by Davis McCarthy

See Also

normalizeCounts, which is used to compute the normalized expression values.

Examples

example_sce <- mockSCE()

# Standard library size normalization:
example_sce2 <- logNormCounts(example_sce)
assayNames(example_sce2)
logcounts(example_sce2)[1:5,1:5]

# Without logging, the assay is 'normcounts':
example_sce2 <- logNormCounts(example_sce, log=FALSE)
assayNames(example_sce2)
normcounts(example_sce2)[1:5,1:5]

# Pre-loading with size factors:
example_sce2 <- computeMedianFactors(example_sce)
example_sce2 <- logNormCounts(example_sce2)
logcounts(example_sce2)[1:5,1:5]

# Also normalizing the alternative experiments:
example_sce2 <- applySCE(example_sce, logNormCounts)
logcounts(altExp(example_sce2))[1:5,1:5]

LTLA/scuttle documentation built on Oct. 28, 2024, 9:45 a.m.