naturalLog<- {ChIPanalyser} | R Documentation |
naturalLog
slot in a
genomicProfileParameters
object.
Setter method for the naturalLog
slot in a
genomicProfileParameters
object.
naturalLog(object)<- value
object |
|
value |
|
During the computation of a Postion Weight Matrix, the
Position Probability Matrix (derived from a Position Frequency Matrix)
is log transformed. This parameter provides whcih "log transform" will be used.
If TRUE, the Natural Log will bu used (ln). If FALSE, log2 will be used.
We strongly encourage to set values when building a
genomicProfileParameters
object.
Returns genomicProfileParameters
object with an updated
value for the naturalLog
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,naturalLog=TRUE) #Setting new Value for naturalLog naturalLog(GPP) <- FALSE