View source: R/preprocessing.R
GetResidual | R Documentation |
This function calls sctransform::get_residuals.
GetResidual(
object,
features,
assay = NULL,
umi.assay = "RNA",
clip.range = NULL,
replace.value = FALSE,
na.rm = TRUE,
verbose = TRUE
)
object |
A seurat object |
features |
Name of features to add into the scale.data |
assay |
Name of the assay of the seurat object generated by SCTransform |
umi.assay |
Name of the assay of the seurat object containing UMI matrix and the default is RNA |
clip.range |
Numeric of length two specifying the min and max values the Pearson residual will be clipped to |
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 |
Returns a Seurat object containing Pearson residuals of added features in its scale.data
get_residuals
## Not run:
data("pbmc_small")
pbmc_small <- SCTransform(object = pbmc_small, variable.features.n = 20)
pbmc_small <- GetResidual(object = pbmc_small, features = c('MS4A1', 'TCL1A'))
## End(Not run)
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