naturalLog_-: Setter method for the 'naturalLog' slot in a...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Setter method for the naturalLog slot in a parameterOptions object.

1	naturalLog(object)<- value

`object`	`object` is a `parameterOptions` 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.

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 parameterOptions 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<e2><80><93>94.

# Loading data
data(ChIPanalyserData)

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