chicagoData {Chicago} | R Documentation

## The `chicagoData` class.

### Description

Constructor for the `chicagoData` class.

### Usage

    chicagoData(...)

### Arguments

`...` | Arguments passed to `new()`.

### Details

While this function can be used to create a `chicagoData` object, most users will use the `setExperiment` function instead.

### Value

A `chicagoData` object has three slots, accessed as follows:

* `intData(cd)` is a data.table (note: not a data.frame) that contains information about fragment pairs. * `settings(cd)` is a list of settings, usually set with the setExperiment() function. For more information about valid settings, please see `defaultSettings`. To modify the settings, use `modifySettings`. * `params(cd)` is a list of parameters. CHiCAGO estimates these automatically, as part of the pipeline.

### Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

### See Also

`setExperiment`, `defaultSettings`

### Examples

      cd <- chicagoData()

[Package Chicago version 1.15.0 Index]