MSnSet_tidiers {biobroom} | R Documentation

## Tidying methods for Biobase's ExpressionSet objects

### Description

Tidying methods for Biobase's ExpressionSet objects

### Usage

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

### Arguments

`x` | MSnSet object
`addPheno` | whether columns should be included in the tidied output for those in the MSnSet's phenoData
`...` | 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

`protein` | protein name
`sample` | sample name (from column names)
`value` | protein quantitation data

### Examples

    if (require("MSnbase")) {
      library(MSnbase)
      # import MSnSet object
      data(msnset)

      # Use tidy to extract genes, sample ids and measured value
      tidy(msnset)
      # add phenoType data
      tidy(msnset, addPheno=TRUE)
    }

[Package biobroom version 1.10.1 Index]