Perform library size normalization on raw counts input. As for the preprocessing step of iNMF integration, by default we don't multiply the normalized values with a scale factor, nor do we take the log transformation. Applicable S3 methods can be found in Usage section.
normalizePeak
is designed for datasets of "atac" modality, i.e. stored
in ligerATACDataset. S3 method for various container object is
not supported yet due to difference in architecture design.
Usage
normalize(object, ...)
# S3 method for matrix
normalize(object, log = FALSE, scaleFactor = NULL, ...)
# S3 method for dgCMatrix
normalize(object, log = FALSE, scaleFactor = NULL, ...)
# S3 method for ligerDataset
normalize(object, chunk = 1000, verbose = getOption("ligerVerbose", TRUE), ...)
# S3 method for liger
normalize(
object,
useDatasets = NULL,
verbose = getOption("ligerVerbose", TRUE),
format.type = NULL,
remove.missing = NULL,
...
)
# S3 method for Seurat
normalize(object, assay = NULL, layer = "counts", save = "ligerNormData", ...)
normalizePeak(
object,
useDatasets = NULL,
verbose = getOption("ligerVerbose", TRUE),
...
)
Arguments
- object
liger object
- ...
Arguments to be passed to S3 methods. The "liger" method calls the "ligerDataset" method, which then calls "dgCMatrix" method.
normalizePeak
directly callsnormalize.dgCMatrix
.- log
Logical. Whether to do a
log(x + 1)
transform on the normalized data. DefaultTRUE
.- scaleFactor
Numeric. Scale the normalized expression value by this factor before transformation.
NULL
for not scaling. Default1e4
.- chunk
Integer. Number of maximum number of cells in each chunk when working on HDF5 file based ligerDataset. Default
1000
.- verbose
Logical. Whether to show information of the progress. Default
getOption("ligerVerbose")
orTRUE
if users have not set.- useDatasets
A character vector of the names, a numeric or logical vector of the index of the datasets to be normalized. Should specify ATACseq datasets when using
normalizePeak
. DefaultNULL
normalizes all valid datasets.- format.type, remove.missing
Deprecated. The functionality of these is covered through other parts of the whole workflow and is no long needed. Will be ignored if specified.
- assay
Name of assay to use. Default
NULL
uses current active assay.- layer
Where the input raw counts should be from. Default
"counts"
. For older Seurat, always retrieve fromcounts
slot.- save
For Seurat>=4.9.9, the name of layer to store normalized data. Default
"ligerNormData"
. For older Seurat, stored todata
slot.
Value
Updated object
.
dgCMatrix method - Returns processed dgCMatrix object
ligerDataset method - Updates the
normData
slot of the objectliger method - Updates the
normData
slot of chosen datasetsSeurat method - Adds a named layer in chosen assay (V5), or update the
data
slot of the chosen assay (<=V4)normalizePeak
- Updates thenormPeak
slot of chosen datasets.