Calculate pearson residuals of features not in the scale.data

This function calls sctransform::get_residuals.

Usage

GetResidual(
  object,
  features,
  assay = NULL,
  umi.assay = "RNA",
  clip.range = NULL,
  replace.value = FALSE,
  na.rm = TRUE,
  verbose = TRUE
)

Arguments

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

Value

Returns a Seurat object containing Pearson residuals of added features in its scale.data

See also

get_residuals

Examples

if (FALSE) { # \dontrun{
data("pbmc_small")
pbmc_small <- SCTransform(object = pbmc_small, variable.features.n = 20)
pbmc_small <- GetResidual(object = pbmc_small, features = c('MS4A1', 'TCL1A'))
} # }