CHiCAGO pipeline function

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Description

This function runs data through the CHiCAGO pipeline.

Usage

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chicagoPipeline(cd, outprefix = NULL, printMemory = FALSE)

Arguments

cd

A chicagoData object.

outprefix

NULL, or a character string. If NULL, diagnostic plots are outputted to the current plotting device. If a character string, then pdfs will be generated for a series of diagnostic plots, in files of form "[outprefix]_[plotname].pdf". For example, outprefix="experiment1" leads to files experiment1_oeNorm.pdf, etc...

printMemory

Set to TRUE for memory diagnostics.

Details

This pipeline runs the following functions in order:

- normaliseBaits

- normaliseOtherEnds

- estimateTechnicalNoise

- estimateDistFun

- estimateBrownianNoise

- getPvals

- getScores

It does not export the output. Use exportResults for this.

Value

An object of class chicagoData.

Warning

The object intData(cd) is updated by reference. Thus, intData(cd) will be altered. See vignette for further information.

Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

See Also

exportResults

Examples

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  ##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)