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Seurat (version 3.1.4)

PrepSCTIntegration: Prepare an object list that has been run through SCTransform for integration

Description

Prepare an object list that has been run through SCTransform for integration

Usage

PrepSCTIntegration(
  object.list,
  assay = NULL,
  anchor.features = 2000,
  sct.clip.range = NULL,
  verbose = TRUE
)

Arguments

object.list

A list of objects to prep for integration

assay

Name or vector of assay names (one for each object) that correspond to the assay that SCTransform has been run on. If NULL, the current default assay for each object is used.

anchor.features

Can be either:

  • A numeric value. This will call SelectIntegrationFeatures to select the provided number of features to be used in anchor finding

  • A vector of features to be used as input to the anchor finding process

sct.clip.range

Numeric of length two specifying the min and max values the Pearson residual will be clipped to

verbose

Display output/messages

Value

An object list with the scale.data slots set to the anchor features