chicagoPipeline {Chicago} | R Documentation |
This function runs data through the CHiCAGO pipeline.
chicagoPipeline(cd, outprefix = NULL, printMemory = FALSE)
cd |
A |
outprefix |
|
printMemory |
Set to |
This pipeline runs the following functions in order:
- getPvals
It does not export the output. Use exportResults
for this.
An object of class chicagoData
.
The object intData(cd)
is updated by reference. Thus, intData(cd)
will be altered. See vignette for further information.
Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett
##Read in some raw data filesDir <- file.path(system.file("extdata", package="Chicago"), "unitTestData") file <- file.path(filesDir, dir(filesDir))[1] print(file) ##we will read in this file designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign") ##Add a setting specific to the unit test data! Do not use in practice! if(!interactive()) { settings <- list(brownianNoise.samples=1) } else { settings <- NULL } cd <- setExperiment(designDir=designDir, settings=settings) cd <- readAndMerge(file, cd)