SE2Tidy: Tidy a SummarizedExperiment Assay

In gabrielodom/pathwayPCA: Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

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.

NOTE: if this function stops working (again), please add a comment here: https://github.com/gabrielodom/pathwayPCA/issues/83

Value

The transposition of the assay in summExperiment to tidy form, with the column data (from the colData slot of the object) appended as the first columns of the data frame.

Examples

   # THIS REQUIRES THE SummarizedExperiment PACKAGE.
   library(SummarizedExperiment)
   data(airway, package = "airway")
   
   airway_df <- SE2Tidy(airway)

gabrielodom/pathwayPCA documentation built on July 10, 2023, 3:32 a.m.