Conditional normalization method (e.g. on GC content) based on approach described in Pickrell, et al, 2010, Nature.

Conditional normalization method (e.g. on GC content) based on approach described in Pickrell, et al, 2010, Nature.

Usage

conditionalNormalize(
  object,
  inputAssay = "counts",
  outputAssay = "normalized",
  conditionalColumn = "GC",
  offsetAssay = NULL,
  bins = 200,
  sizeFactors = NULL,
  minCount = 1,
  minSamples = 1,
  aggregate.fn = sum
)

Arguments

object

A SummarizedExperiment object.

inputAssay

The name of the assay to use for the calculation.

outputAssay

The name of the assay to use for the output.

conditionalColumn

The column in the metadata to use for the conditional normalization.

offsetAssay

The name of the assay to use for the offset.

bins

The number of bins to use for the conditional normalization.

sizeFactors

The size factors to use for the normalization.

minCount

The minimum count to consider a unit (CTSS, gene, etc.) as expressed.

minSamples

The minimum number of samples to consider a unit as expressed.

aggregate.fn

The function to use for aggregation.

Value

A SummarizedExperiment object with the normalized counts.