thetaThreshold {ChIPanalyser}R Documentation

Accessor method for the thetaThreshold slot in a occupancyProfileParameters object

Description

Accessor method for the thetaThreshold slot in a occupancyProfileParameters object

Usage

thetaThreshold(object)

Arguments

object

object is a occupancyProfileParameters object

Details

In order to measure the accuracy of predicted models agaisnt real ChIP-seq data, ChIPanalyser uses three "measures": correlation, Mean Squared Error and Theta. Theta is an in house metric that can be described as a modified ratio of correlation over Mean Squarred Error. The higher the value of theta , the better the fit becomes. The theta threshold serves the purpose of avoiding extreme values and thus clarifying optimal parameter heat maps ( see plotOptimalHeatMaps). Default is set at 0.1

Value

Returns the value assigned to the thetaThreshold slot in a occupancyProfileParameters

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.

Examples

# Building occupancyProfileParameters object
OPP <- occupancyProfileParameters()
#Setting new Value for thetaThreshold
thetaThreshold(OPP)

[Package ChIPanalyser version 1.2.0 Index]