SCTAssay-class | R Documentation |
The SCTModel object is a model and parameters storage from SCTransform. It can be used to calculate Pearson residuals for new genes.
The SCTAssay object contains all the information found in an Assay
object, with extra information from the results of SCTransform
## S3 method for class 'SCTAssay'
levels(x)
## S3 replacement method for class 'SCTAssay'
levels(x) <- value
x |
An |
value |
New levels, must be in the same order as the levels present |
levels
: SCT model names
levels<-
: x
with updated SCT model names
feature.attributes
A data.frame with feature attributes in SCTransform
cell.attributes
A data.frame with cell attributes in SCTransform
clips
A list of two numeric of length two specifying the min and max values the Pearson residual will be clipped to. One for vst and one for SCTransform
umi.assay
Name of the assay of the seurat object containing UMI matrix and the default is RNA
model
A formula used in SCTransform
arguments
other information used in SCTransform
median_umi
Median UMI (or scale factor) used to calculate corrected counts
SCTModel.list
A list containing SCT models
SCT results are named by initial run of SCTransform
in order
to keep SCT parameters straight between runs. When working with merged
SCTAssay
objects, these model names are important. levels
allows querying the models present. levels<-
allows the changing of
the names of the models present, useful when merging SCTAssay
objects.
Note: unlike normal levels<-
, levels<-.SCTAssay
allows complete changing of model names, not reordering.
SCTAssay
from an Assay
Conversion from an Assay
object to an SCTAssay
object by
is done by adding the additional slots to the object. If from
has
results generated by SCTransform
from Seurat v3.0.0 to v3.1.1,
the conversion will automagically fill the new slots with the data
Assay
Assay
## Not run:
# SCTAssay objects are generated from SCTransform
pbmc_small <- SCTransform(pbmc_small)
## End(Not run)
## Not run:
# SCTAssay objects are generated from SCTransform
pbmc_small <- SCTransform(pbmc_small)
pbmc_small[["SCT"]]
## End(Not run)
## Not run:
# Query and change SCT model names
levels(pbmc_small[['SCT']])
levels(pbmc_small[['SCT']]) <- '3'
levels(pbmc_small[['SCT']])
## End(Not run)
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