normalize-SummarizedExperiment-method: Normalize the 'assays' in a 'SummarizedExperiment' Object
In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description Usage Arguments Details Value See Also

Normalize the assays in a SummarizedExperiment Object

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

`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.

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

The SummarizedExperiment with one or more of the matrices in assays normalized and the normalization details in the normalization item of the object metadata.

preprocessCaret, caret::preProcess

bhklab/PDATK documentation built on Dec. 27, 2021, 7:46 a.m.