SummarizedExperiment_tidiers: Tidying methods for Biobase's SummarizedExperiment objects

In StoreyLab/biobroom: Turn Bioconductor objects into tidy data frames

Description

Tidying methods for Biobase's SummarizedExperiment objects

Usage

## S3 method for class 'RangedSummarizedExperiment'
tidy(x, addPheno = FALSE,
  assay = SummarizedExperiment::assayNames(x)[1L], ...)

Arguments

x	SummarizedExperiment object
addPheno	whether columns should be included in the tidied output for those in the SummarizedExperiment colData
assay	Which assay to return as the value column. Defaults to assays(x)[[1L]]
...	extra arguments (not used)

Details

addPheno=TRUE adds columns that are redundant (since they add per-sample information to a per-sample-per-gene data frame), but that are useful for some kinds of graphs and analyses.

Value

tidy returns a data frame with one row per gene-sample combination, with columns

gene	gene name
sample	sample name (from column names)
value	expressions

If addPheno is TRUE then information from colData is added.

Examples

if (require("SummarizedExperiment", "airway")) {
    data(airway)

    se <- airway
    tidy(se)
}

StoreyLab/biobroom documentation built on May 9, 2019, 3:09 p.m.