logNormCounts {scuttle} | 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 = 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 )
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.
This is retained for back-compatibility and will override any setting of |
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 |
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 |
normalize.all |
Logical scalar indicating whether to return normalized values for all genes.
If |
assay.type |
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 |
size_factors |
Soft-deprecated equivalents to the arguments described previously. |
pseudo_count |
Soft-deprecated equivalents to the arguments described previously. |
center_size_factors |
Soft-deprecated equivalents to the arguments described previously. |
exprs_values |
Soft-deprecated equivalents to the arguments described previously. |
use.altexps, use_altexps |
Deprecated, use |
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
.
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
.
Aaron Lun, based on code by Davis McCarthy
normalizeCounts
, which is used to compute the normalized expression values.
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]