attributes {IntEREst} | R Documentation

## Extracting values of useful attributes of SummarizedExperiment objects

### Description

Several functions are provided that can extract various attribnutes from an object of class `SummarizedExperiment` generated by IntEREst functions, e.g. `interest()`, `interest`, and `readInterestResults`. It is possible to extract sample annotations using `getAnnotation` function. One can also extract the scaled retention levels of the introns/exons using `scaledRetention()` function. Notes that `colData` and `rowData` methods of `SummarizedExperiment` class can also be used to extract row and column data.

### Usage

    getAnnotation(x)
    scaledRetention(x)

### Arguments

`x` | Object of type `SummarizedExperiment`.

### Value

Various data types (data.frame/vector) dependent on the function used. See the "Description" for more information.

### Author(s)

Ali Oghabian

### See Also

`SummarizedExperiment-class` `addAnnotation` `counts-method` `plot-method`

### Examples

    # Retrieve the sample annotations from mdsChr22Obj
    getAnnotation(mdsChr22Obj)
    # Retrieving the scaled retention levels from mdsChr22Obj
    head(scaledRetention(mdsChr22Obj))

    #for row and column data SummarizedExperiment methods can be used
    head(rowData(mdsChr22Obj))
    colData(mdsChr22Obj)

[Package IntEREst version 1.11.5 Index]