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`.

### See Also

`preprocessCaret`, `caret::preProcess`

[Package PDATK version 1.2.0 Index]