noOfSites: Accessor Method for the 'noOfSites' slot in a...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

noOfSites

R Documentation

Accessor Method for the `noOfSites` slot in a `parameterOptions` object

Description

Accessor Method for the noOfSites slot in a parameterOptions object

Usage

noOfSites(object)

Arguments

object

object is parameterOptions object

Details

While computing Position Weight Matricies (PWM) from Position Frequency Matricies (PFM), it is possible to restrict the number of sites that will be used to compute the PWM. The default is set at "all". In this case, all sites will be used to compute the PWM.

Value

Returns the value assigned to the noOfSites slot in a parameterOptions 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)

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

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.