occupancyProfileParameters {ChIPanalyser}R Documentation

Occupancy Profile Parameters

Description

occupancyProfileParameters is a parameter storage object. Similarly to genomicProfileParameters, this object serves the purpose of handling the set of parameters needed when using certain functions.

Usage


occupancyProfileParameters(ploidy = 2 , boundMolecules = 1000 ,
    backgroundSignal = 0 ,  maxSignal = 1 , chipMean = 150 ,
    chipSd = 150 , chipSmooth = 250 , stepSize = 10 ,
    removeBackground = 0 )

Arguments

ploidy

ploidy: A numeric Value descibing the ploidy of the organism. Default: 2

boundMolecules

boundMolecules: A vector (or single value) containing the number of bound Molecules (bound Transcription Factors): Default: 1000

backgroundSignal

backgroundSignal: A numeric value descibing the ChIP-seq background Signal (average signal from real ChIP seq data). Default: 0

maxSignal

maxSignal: A numeric value describing the highest ChIP-seq signal (from real ChIP-seq data). Default: 1

chipMean

chipMean: A numeric value describing the mean width of a ChIP- seq peak: Default:150

chipSd

chipSd: A numeric value describing the standard deviation of ChIP-seq peaks. Default: 150

chipSmooth

chipSmooth: A numeric value describing the width of the window used to smooth Occupancy profiles into ChIP profiles. Default:250

stepSize

stepSize: A numeric value describing the step Size (in base pairs) between each ChIP-seq score. Default:10 (Scored every 10 base pairs)

removeBackground

removeBackground: A numeric value describing the value at which score should be removed. Defualt:0 (If negative scores then remove)

Details

The purpose of this occupancyProfileParameters object is to store paramters used duing certin of the functions available in ChIPanalyser. As opposed to genomicProfileParameters, this object is not required for a function to run as all paramters have default values ( the object will be created internally as default values will be used - This also means that no argument is required for this object to be built). However, it is strongly advised to set these parameters to increase the goodness of fit between the predicted Profiles and the real ChIP-seq profiles. As an example, maxSignal is the maximum signal of the real ChIP-seq data, this signal will depend on the data being used thus should be tuned to opimise the model.

Default values are set at:

ploidy = 2

boundMolecules = 1000

backgroundSignal = 0

maxSignal = 1

chipMean = 150

chipSd = 150

chipSmooth = 250

stepSize = 10

removeBackground = 0

Value

Returns a occupancyProfileParameters object

Author(s)

Patrick C. N. Martin <pm16057@essex.ac.uk>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

See Also

occupancyProfileParameters-class genomicProfileParameters genomicProfileParameters-class

Examples

OPP <- occupancyProfileParameters()
# OR
OPP <- occupancyProfileParameters(ploidy=2,
    boundMolecules=5000,backgroundSignal=0)


[Package ChIPanalyser version 1.6.0 Index]