naturalLog: Accessor method the 'naturalLog' slot in a 'parameterOptions'...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Accessor method the naturalLog slot in a parameterOptions object.

1	naturalLog(object)

object

object is parameterOptions object.

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 parameterOptions object.

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

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<e2><80><93>94.

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions(naturalLog=TRUE)
#Setting new Value for naturalLog
naturalLog(GPP)