tidy.deSet {biobroom} | R Documentation

## Tidying methods for edge's deSet object

### Description

Tidying methods for edge's deSet object

### Usage

    ## S3 method for class 'deSet'
    tidy(x, addPheno = FALSE, ...)

    ## S3 method for class 'deSet'
    augment(x, data, ...)

    ## S3 method for class 'deSet'
    glance(x, ...)

### Arguments

`x` | deSet object
`addPheno` | whether columns should be included in the tidied output for those in the ExpressionSet's phenoData
`...` | extra arguments (not used)
`data` | Original data can be added. Default is NULL.

### 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 on log2 scale

`augment` returns a data.frame with

`p.value` | the original p-values given to `qvalue`
`q.value` | the computed q-values
`lfdr` | the local false discovery rate

`glance` returns a data.frame with the model fits

[Package biobroom version 1.10.1 Index]