logNormCounts {scater} | R Documentation |
Compute log-transformed normalized expression values from a count matrix in a SingleCellExperiment object.
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() )
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 |
size_factors |
A numeric vector of cell-specific size factors.
Alternatively |
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 |
name |
String containing an assay name for storing the output normalized values.
Defaults to |
BPPARAM |
A BiocParallelParam object specifying how library size factor calculations should be parallelized.
Only used if |
use_altexps |
Logical scalar indicating whether normalization should be performed for alternative experiments in Alternatively, a character vector specifying the names of the alternative experiments to be normalized. Alternatively, |
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.
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
.
Aaron Lun, based on code by Davis McCarthy
normalizeCounts
, which is used to compute the normalized expression values.
example_sce <- mockSCE() example_sce <- logNormCounts(example_sce) assayNames(example_sce)