chicagoData: The 'chicagoData' class.

In Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

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()

Example output

Loading required package: data.table

Welcome to CHiCAGO - version 1.18.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")

Chicago documentation built on Nov. 8, 2020, 8:15 p.m.