Ensure marker genes are in the scale.data layer of an assay of the Seurat object

Values added for the missing features are clamped to a range resolved as: the clip.range argument when one is given, otherwise the range the scalers recorded in @misc$scale_clip[[assay]], otherwise the c(-10, 10) default. Pass NULL or a range of Inf to add the values uncapped. The range applies to both the z-scores of an RNA assay and the residuals of an SCT assay; for the latter a recorded range (e.g. the clip of the SCT models) is normally wider than the +/- 10 default and wins over it.

Usage

EnsureSeuratScaleData(
  object,
  features,
  assay = NULL,
  umi_assay = "RNA",
  clip.range = c(-10, 10)
)

Arguments

object

Seurat object

features

Character vector, or a list of character vectors, of feature names to ensure in the scale.data layer

assay

Assay to use. If NULL, the default assay will be used.

umi_assay

Assay to use for the UMI counts. Default is "RNA". This is used to get the counts for scaling.

clip.range

Numeric vector of length 2: the lower and upper bound applied to the added values, in the units of the scale.data layer (z-scores, or residuals for an SCT assay). Inf means unbounded. When omitted, the range recorded in object@misc$scale_clip[[assay]] is reused, falling back to the c(-10, 10) default. Pass NULL (or c(-Inf, Inf)) to clamp nothing.

Value

The Seurat object with the features ensured in the scale.data layer