extractExpressionClass {CAGEr} | R Documentation

## Extract elements of the specified expression class

### Description

Extracts CTSSs or consensus clusters belonging to a specified expression class.

### Usage

    extractExpressionClass(object, what, which = "all")

    ## S4 method for signature 'CAGEexp'
    extractExpressionClass(object, what, which = "all")

    ## S4 method for signature 'CAGEset'
    extractExpressionClass(object, what, which = "all")

### Arguments

`object` | A `CAGEset` object.
`what` | Which level of expression clustering should be used. Can be either `"CTSS"` to extract expression class of individual CTSSs or `"consensusClusters"` to extract expression class of consensus clusters.
`which` | Which expression class should be extracted. It has to be one of the valid expression class labels (as returned by `expressionClasses` function), or `"all"` to extract members of all expression classes.

### Value

Returns a `data.frame` of CTSSs (when `what = "CTSS"`) or consensus clusters (when `what = "consensusClusters"`) belonging to a specified expression class, with genomic coordinates and additional information. Last column contains the label of the corresponding expression class.

### Author(s)

Vanja Haberle

### See Also

`getExpressionProfiles`, `plotExpressionProfiles`, `expressionClasses`.

### Examples

    CTSSexprClasses <- extractExpressionClass(exampleCAGEset, what = "CTSS", which = "all")
    head(CTSSexprClasses)

[Package CAGEr version 1.30.3 Index]