chicagoPipeline: CHiCAGO pipeline function

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

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)

Example output

Loading required package: data.table

Welcome to CHiCAGO - version 1.4.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
[1] "/usr/local/lib/R/site-library/Chicago/extdata/unitTestData/unitTest_mESC_rep1.chinput"
Locating <baitmapfile>.baitmap in /usr/local/lib/R/site-library/Chicago/extdata/unitTestDesign...
Found unitTest.baitmap
Locating <rmapfile>.rmap in /usr/local/lib/R/site-library/Chicago/extdata/unitTestDesign...
Found unitTest.rmap
Locating <nperbinfile>.npb in /usr/local/lib/R/site-library/Chicago/extdata/unitTestDesign...
Found unitTest.npb
Locating <nbaitsperbinfile>.nbpb in /usr/local/lib/R/site-library/Chicago/extdata/unitTestDesign...
Found unitTest.nbpb
Locating <proxOEfile>.poe in /usr/local/lib/R/site-library/Chicago/extdata/unitTestDesign...
Found unitTest.poe
Checking the design files...
Reading /usr/local/lib/R/site-library/Chicago/extdata/unitTestData/unitTest_mESC_rep1.chinput
Processing input...
minFragLen = 150 maxFragLen = 40000
Filtered out 58 interactions involving other ends < minFragLen or > maxFragLen.
minNPerBait = 250
Filtered out 3 baits with < minNPerBait reads.

Removed interactions with fragments adjacent to baits.
Filtered out 0 baits without proximal non-Bait2bait interactions

Merging samples...
Computing merged scores...

Computing sample scaling factors...

Reading NPerBin file...
Computing normalisation scores...

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