| ScalingFactorPWM<- {ChIPanalyser} | R Documentation |
lambda slot in a
genomicProfileParameters object
Setter method for the lambda slot in a
genomicProfileParameters object
ScalingFactorPWM(object) <- value
object |
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value |
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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)