setExperiment: Set Experiment

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

Description

Creates a template CHiCAGO experiment object. This should be the first function called.

Usage

setExperiment(designDir = "", settings = list(),
      settingsFile = NULL, def.settings=defaultSettings())

Arguments

designDir	The location of the design directory, e.g "~/resources/path". (Should not end with a slash.)
settings	A named list containing settings to apply. Setting names(settings)[1] is set to (settings)[[1]], and so on. This overrides anything specified in settingsFile, or in def.settings.
settingsFile	The location of a file containing settings. Each row should contain the name of a setting, followed by whitespace, followed by the value of that setting. Overrides anything specified in def.settings.
def.settings	These are the default settings.

Details

For a list of settings, see defaultSettings.

Value

An object of class chicagoData.

Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

See Also

defaultSettings

Examples

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

  cd <- setExperiment(designDir)

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