Calculate batch support for expression data.

Calculate batch support for expression data.

Usage

calcBatchSupport(
  object,
  batch,
  inputAssay = "counts",
  outputColumn = "batchSupport",
  unexpressed = 0,
  minSamples = 1
)

Arguments

object

A SummarizedExperiment object.

batch

A factor indicating the batch of each sample.

inputAssay

The assay to use.

outputColumn

The name of the column to store the batch support.

unexpressed

The threshold below which a unit (CTSS, gene, etc.) is considered unexpressed.

minSamples

The minimum number of samples in which a unit must be expressed to be considered supported.

Value

A SummarizedExperiment object with the batch support column.