SE2Tidy {pathwayPCA} | R Documentation

## Tidy a SummarizedExperiment Assay

### Description

Extract the assay information from a `SummarizedExperiment-class`-object, transpose it, and and return it as a tidy data frame that contains assay measurements, feature names, and sample IDs

### Usage

    SE2Tidy(summExperiment, whichAssay = 1)

### Arguments

`summExperiment` | A `SummarizedExperiment-class` object
`whichAssay` | Because `SummarizedExperiment` objects can store multiple related assays, which assay will be paired with a given pathway collection to create an `Omics*`-class data container? Defaults to 1, for the first assay in the object.

### Details

This function is designed to extract and transpose a "tall" assay data frames (where genes or proteins are the rows and patient or tumour samples are the columns) from a `SummarizedExperiment` object. This function also transposes the row (feature) names to column names and the column (sample) names to row names via the `TransposeAssay` function.

### Value

The transposition of the assay in `summExperiment` to tidy form

### Examples

       # THIS REQUIRES THE SummarizedExperiment PACKAGE.
       library(SummarizedExperiment)
       data(airway, package = "airway")

       airway_df <- SE2Tidy(airway)

[Package pathwayPCA version 1.6.3 Index]