FetchResiduals | R Documentation |
This function calls sctransform::get_residuals.
FetchResiduals(object, ...)
## S3 method for class 'Seurat'
FetchResiduals(
object,
features,
assay = NULL,
umi.assay = "RNA",
layer = "counts",
clip.range = NULL,
reference.SCT.model = NULL,
replace.value = FALSE,
na.rm = TRUE,
verbose = TRUE,
...
)
## S3 method for class 'SCTAssay'
FetchResiduals(
object,
umi.object,
features,
layer = "counts",
clip.range = NULL,
reference.SCT.model = NULL,
replace.value = FALSE,
na.rm = TRUE,
verbose = TRUE,
...
)
object |
An SCTAssay object. |
... |
Arguments passed to other methods (not used) |
features |
Name of features to fetch residuals for. |
assay |
Name of the assay to fetch residuals for. |
umi.assay |
Name of the assay of the seurat object containing counts matrix to use when recalculating any missing residuals. |
layer |
The name of the layer(s) in 'umi.assay' to use when recalculating any missing residuals. |
clip.range |
Numeric of length two specifying the min and max values the Pearson residual will be clipped to. |
reference.SCT.model |
If provided, the reference model will be used to recalculate missing residuals instead of the |
replace.value |
Recalculate residuals for all features, even if they are already present. Useful if you want to change the clip.range. |
na.rm |
For features where there is no feature model stored, return NA for residual value in scale.data when na.rm = FALSE. When na.rm is TRUE, only return residuals for features with a model stored for all cells. |
verbose |
Whether to print messages and progress bars |
umi.object |
TK. |
A matrix containing the requested pearson residuals.
get_residuals
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