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