estimateTechnicalNoise: Estimate Technical Noise

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

Description

Calculates the expected technical noise based on trans read pairs.

Usage

estimateTechnicalNoise(cd, plot = TRUE, outfile = NULL)

Arguments

cd	A chicagoData object.
plot	Logical - if TRUE, then output a diagnostic plot.
outfile	NULL, or a character string. If NULL, the diagnostic plot is outputted to the current plotting device. If a character string, e.g. outfile="tech.pdf", then the plot will be outputted to that file.

Value

An object of class chicagoData, with additional columns "tlb", "tblb", "Tmean".

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

chicagoPipeline

Examples

data(cdUnitTest)

##modifications to cdUnitTest, ensuring it uses correct design directory
designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

cdUnitTest <- estimateTechnicalNoise(cdUnitTest)

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")
Warning: settings are not checked for consistency with the original ones.
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...
Estimating technical noise based on trans-counts...
Binning baits based on observed trans-counts...
Defining interaction pools and gathering the observed numbers of trans-counts per pool...
Computing the total number of possible interactions per pool...
Preparing the data.....
Processing fragment pools...
Plotting...
Post-processing the results...
Warning message:
In estimateTechnicalNoise(cdUnitTest) :
  Columns will be overwritten: tblb, Tmean

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