RunCanek {Canek}

RunCanek

Description

Runs Canek integration.

Usage

RunCanek(x, ...)

## S3 method for class 'Seurat'
RunCanek(
  x,
  batches = NULL,
  slot = "data",
  assay = NULL,
  features = NULL,
  selection.method = "vst",
  nfeatures = 2000,
  fvf.nfeatures = 2000,
  integration.name = "Canek",
  debug = FALSE,
  ...
)

## S3 method for class 'SingleCellExperiment'
RunCanek(
  x,
  batches = NULL,
  assay = "logcounts",
  integration.name = "Canek",
  debug = FALSE,
  ...
)

## S3 method for class 'list'
RunCanek(x, ...)

Arguments

x

object with expression counts or list of matrices.

...

additional arguments passed down to methods.

batches

for S4 objects the column containing batch information.

slot

slot used for Seurat objects (default: data).

assay

assay used for Seurat objects.

features

optional vector of features to use for correction.

selection.method

method used for FindVariableFeatures on Seurat objects when features is NULL.

nfeatures

number of features returned by SelectIntegrationFeatures.

fvf.nfeatures

number of features returned by FindVariableFeatures.

integration.name

name for the integrated assay.

debug

whether to store information about correction vector.

Value

An object of the appropriate type.