ScalingFactorPWM<- {ChIPanalyser} | R Documentation |
lambda
slot in a
genomicProfileParameters
object
Setter method for the lambda
slot in a
genomicProfileParameters
object
ScalingFactorPWM(object) <- value
object |
|
value |
|
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
).
Returns a genomicProfileParameters
object with an updated
value for the lambda
slot.
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.
# 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)