Normalise Other Ends

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Description

Compute s_i normalisation factors for other ends, and normalised counts.

Usage

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normaliseOtherEnds(cd, Ncol = "NNb", normNcol = "NNboe", plot = TRUE, outfile = NULL)

Arguments

cd

A chicagoData object.

Ncol

The name of an input column in intData(cd) that contains counts normalised by bait (i.e. it is output from normaliseBaits.

normNcol

The name of an output column that will contain counts normalised by other ends (in addition to any normalisation already performed on the Ncol column). Useful for plotting.

plot

If TRUE, 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.

Details

A chicagoData object: intData(cd) gains new columns s_i, and normalised output NNboe (unless the normNcol parameter is altered).

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

Examples

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##FIXME: example can be run by loading data package if it is installed, once it exists

if("PCHiCdata" %in% rownames(installed.packages()))
{
  library(PCHiCdata)
  data(smESC)
  
  ##modifiy smESC to use correct design directory
  designDir <- file.path(system.file("extdata", package="PCHiCdata"), "mm9TestDesign")
  smESC <- modifySettings(cd=smESC, designDir=designDir)
  
  ##normalise here...
  normaliseOtherEnds(smESC)
  
} else {
  warning("Please install the PCHiCdata package to run this example.")
}