Calculate pearson residuals of features not in the scale.data
This function calls sctransform::get_residuals.
GetResidual( object, features, assay = NULL, umi.assay = NULL, 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
data("pbmc_small")
pbmc_small <- SCTransform(object = pbmc_small, variable.features.n = 20)
pbmc_small <- GetResidual(object = pbmc_small, features = c('MS4A1', 'TCL1A'))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.