SummarizedExperiment_tidiers {biobroom} | R Documentation

## Tidying methods for Biobase's SummarizedExperiment objects

### 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)
    }

[Package biobroom version 1.10.1 Index]