FetchResiduals: Calculate pearson residuals of features not in the scale.data

In satijalab/seurat: Tools for Single Cell Genomics

Calculate pearson residuals of features not in the scale.data

Description

This function calls sctransform::get_residuals.

Usage

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
)

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
layer	Name (prefix) of the layer to pull counts from
clip.range	Numeric of length two specifying the min and max values the Pearson residual will be clipped to
reference.SCT.model	reference.SCT.model If a reference SCT model should be used for calculating the residuals. When set to not NULL, ignores the 'SCTModel' paramater.
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

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.