ScalingFactorPWM<- {ChIPanalyser}R Documentation

Setter method for the lambda slot in a genomicProfileParameters object

Description

Setter method for the lambda slot in a genomicProfileParameters object

Usage

ScalingFactorPWM(object) <- value


Arguments

object

object is a genomicProfileParameters object

value

value is a positive numeric value or a vector of positive numeric values that will be assigned to the lambda slot in a genomicProfileParameters object. Default is set at 1

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 a genomicProfileParameters object with an updated value for the lambda slot.

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))
#Setting New value for ScalingFactorPWM
ScalingFactorPWM(GPP) <- 2
#OR
ScalingFactorPWM(GPP) <- c(2,3,4)

[Package ChIPanalyser version 1.4.0 Index]