thetaThreshold {ChIPanalyser} | R Documentation |
thetaThreshold
slot in a
occupancyProfileParameters
object
Accessor method for the thetaThreshold
slot in a
occupancyProfileParameters
object
thetaThreshold(object)
object |
|
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
Returns the value assigned to the thetaThreshold
slot in
a occupancyProfileParameters
Patrick C. N. Martin <pm16057@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
# Building occupancyProfileParameters object OPP <- occupancyProfileParameters() #Setting new Value for thetaThreshold thetaThreshold(OPP)