chicagoPipeline {Chicago} | R Documentation

## CHiCAGO pipeline function

### Description

This function runs data through the CHiCAGO pipeline.

### Usage

    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

      ##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)

[Package Chicago version 1.14.0 Index]