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

Description Usage Arguments Details Value Author(s) See Also Examples

Modify the settings in a chicagoData object.

1	modifySettings(cd, designDir=NULL, settings=list(), settingsFile=NULL)

`cd`	A `chicagoData` object.
`designDir`	The new location of the design directory, e.g "~/resources/path" or NULL if not modified.
`settings`	A named list containing settings to modify.
`settingsFile`	The location of a file containing settings or NULL if not provided. Each row should contain the name of a setting, followed by whitespace, followed by the value of that setting.

cd's settings are updated. For a list of available settings, see defaultSettings.

An object of class chicagoData.

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

setExperiment, defaultSettings

designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")

cd <- setExperiment(designDir)

##Suppose I want to change the number of samples drawn for dispersion estimation 
print(settings(cd)$brownianNoise.subset)

cd <- modifySettings(cd, settings=list(brownianNoise.subset = 10))
print(settings(cd)$brownianNoise.subset)