R: Compute log-normalized expression values

logNormCounts {scater}

R Documentation

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 = TRUE,
  pseudo_count = 1,
  center_size_factors = TRUE,
  ...,
  exprs_values = "counts",
  name = NULL,
  BPPARAM = SerialParam()
)

## S4 method for signature 'SingleCellExperiment'
logNormCounts(
  x,
  size_factors = NULL,
  log = TRUE,
  pseudo_count = 1,
  center_size_factors = TRUE,
  ...,
  exprs_values = "counts",
  use_altexps = FALSE,
  name = NULL,
  BPPARAM = SerialParam()
)

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 extracted or computed from `x`.
`log`	Logical scalar indicating whether normalized values should be log2-transformed.
`pseudo_count`	Numeric scalar specifying the pseudo_count to add when log-transforming expression values.
`center_size_factors`	Logical scalar indicating whether size factors should be centered at unity before being used.
`exprs_values`	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 `log=TRUE` and `"normcounts"` otherwise.
`BPPARAM`	A BiocParallelParam object specifying how library size factor calculations should be parallelized. Only used if `size_factors` is not specified.
`use_altexps`	Logical scalar indicating whether normalization should be performed for alternative experiments in `x`. Alternatively, a character vector specifying the names of the alternative experiments to be normalized. Alternatively, `NULL` in which case alternative experiments are not used.

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 x is a SingleCellExperiment that contains alternative Experiments, normalized values can be computed and stored within each alternative experiment by setting use_altexps appropriately. By default, use_altexps=FALSE to avoid problems from attempting to library size-normalize alternative experiments that have zero total counts for some cells.

If size_factors=NULL, size factors are obtained following the rules in normalizeCounts. This is done independently for the main and alternative Experiments when use_altexps is specified, i.e. no information is shared between Experiments by default. However, if size_factors is supplied, it will override any size factors available in any Experiment.

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.

If x contains alternative experiments and use_altexps=TRUE, each of the alternative experiments in x will also contain an additional assay. This can be limited to particular altExps entries by specifying them in use_altexps.

Author(s)

Aaron Lun, based on code by Davis McCarthy

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
assayNames(example_sce)

[Package scater version 1.16.2 Index]