R: Normalize the 'assays' of a 'MutliAssayExperiment' Object

normalize,MultiAssayExperiment-method {PDATK}

R Documentation

Normalize the `assays` of a `MutliAssayExperiment` Object

Description

For this method to work, there must be a normalize method defined for all classes of experiments in the MultiAssayExperiment

Usage

## S4 method for signature 'MultiAssayExperiment'
normalize(
  object,
  MARGIN = 2,
  FUN = "preprocessCaret",
  ...,
  whichAssays = seq_along(assays(object))
)

Arguments

`object`	A `SummarizedExperiment` object with assays to normalize.
`MARGIN`	An `integer` indicating if rows (1) or columns (2) should be normalized. Defaults to 2 for columns.
`FUN`	A function to normalize your data with. Should accept a rectangular object such as a `matrix`, `data.frame`, or `data.table` and return an object of the same class with the data normalized using FUN.
`...`	Fall through parameters to FUN. For the default FUN, these are passed to `caret::preProcess` to allow configuration of the normalization method. Omitting any arguments with the default FUN will scale and center the data.
`whichAssays`	A `numeric` or `character` vector specifying the indices of the assays to normalize. Defaults to all assays.

Details

When using the default FUN, it is also possible to impute missing values. See ?caret::preProcess for information on available methods.

Value

The MultiAssayExperiment with one or more of the assays normalized and information about the normalization method in the normalization item of the object metadata.