normaliseOtherEnds {Chicago} | R Documentation

## Normalise Other Ends

### Description

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

### Usage

    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

    ##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.")
    }

[Package Chicago version 1.20.0 Index]