ExpressionSet_tidiers {biobroom} | R Documentation

## Tidying methods for Biobase's ExpressionSet objects

### Description

Tidying methods for Biobase's ExpressionSet objects

### Usage

    ## S3 method for class 'ExpressionSet'
    tidy(x, addPheno = FALSE,
      assay = Biobase::assayDataElementNames(x)[1L], ...)

### Arguments

`x` | ExpressionSet object
`addPheno` | whether columns should be included in the tidied output for those in the ExpressionSet's phenoData
`assay` | The name of the `assayDataElement` to use as the values to tidy. Defaults to `assayDataElementNames(x)[1L]`, which is usually equivalent to `exprs(x)`.
`...` | 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 on log2 scale

### Examples

    library(Biobase)
    # import ExpressionSet object
    data(hammer)

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

[Package biobroom version 1.10.1 Index]