naturalLog<- {ChIPanalyser}R Documentation

Setter method for the naturalLog slot in a genomicProfileParameters object.

Description

Setter method for the naturalLog slot in a genomicProfileParameters object.

Usage

naturalLog(object)<- value

Arguments

object

object is a genomicProfileParameters object.

value

value is a logical value that will determine if the natural log or log2 should be used for the computation of the Position Weight Matrix.

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 genomicProfileParameters object with an updated value for the naturalLog slot.

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) <- FALSE
[Package ChIPanalyser version 1.2.0 Index]