Accessor method the naturalLog slot in a genomicProfileParameters object.

Description

Accessor method the naturalLog slot in a genomicProfileParameters object.

Usage

naturalLog(object)

Arguments

Details

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.

Value

Returns the value assigned to the naturalLog slot in a genomicProfileParameters object.

Author(s)

Patrick C.N. Martin <p.martin@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,naturalLog=TRUE)
#Setting new Value for naturalLog
naturalLog(GPP)