ScalingFactorPWM {ChIPanalyser}R Documentation

Accessor method for the lambda slot in a genomicProfileParameters object

Description

Accessor method for the lambda slot in a genomicProfileParameters object

Usage

ScalingFactorPWM(object)

Arguments

object

object is a genomicProfileParameters object

Details

The model used in ChIPanalyser relies on a scaling factor (scaling Transcription Factor binding affinity) for the PWM Score (or binding energy). It is also referred to as lambda. In the case a vector of values is provided, each value will be either computed individually ( as it will be the case in computeGenomeWidePWMScore) or in combination with boundMolecules (as it will be the case in computeOccupancy).

Value

Returns the value or vector assigned to the lambda slot in a genomicProfileParameters 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.

Examples

# Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building data objects
GPP <- genomicProfileParameters(PFM=PFM, ScalingFactorPWM=c(0.5,1,1.5))
#Accessing value for ScalingFactorPWM
ScalingFactorPWM(GPP)

[Package ChIPanalyser version 1.2.0 Index]