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

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