normalize,SummarizedExperiment-method {PDATK} | R Documentation

## Normalize the `assays` in a `SummarizedExperiment` Object

### Description

Normalize the `assays` in a `SummarizedExperiment` Object

### Usage

    ## S4 method for signature 'SummarizedExperiment'
    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 columns. Defaults to 2.
`FUN` | A function to normalize your data with. The function should accept a matrix, normalize the columns then return a matrix. The data will be transposed before applyying FUN if MARGIN=1.
`...` | Fall through parameters to FUN. When using the default FUN, the data is scaled and centered when no additional arguments are specified.
`whichAssays` | A `numeric` or `character` vector specifying the indices or names 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 `SummarizedExperiment` with one or more of the matrices in `assays` normalized and the normalization details in the `normalization` item of the object `metadata`.

### See Also

`preprocessCaret`, `caret::preProcess`

[Package PDATK version 1.0.2 Index]