noOfSites<- {ChIPanalyser} | R Documentation |
noOfSites
slot in a
genomicProfileParameters
object.
Setter Method for the noOfSites
slot in a
genomicProfileParameters
object.
noOfSites(object) <- value
object |
|
value |
|
While computing Position Weight Matricies (PWM) from Position Frequency Matricies (PFM), it is possible to restrict the number of sites that will be used to compute the PWM. The default is set at 0. In this case, all sites will be used to compute the PWM.
Returns a genomicProfileParameters
object with an updated
value for the noOfSites
slot.
Patrick C.N. Martin <p.martin@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,noOfSites=0) #Setting new Value for naturalLog noOfSites(GPP) <- 8