chicagoPipeline: CHiCAGO pipeline function

Description

This function runs data through the CHiCAGO pipeline.

Usage

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

Arguments

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.

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.

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.

Examples

Run this code

  ##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)

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