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

noOfSites<-

R Documentation

Setter Method for the `noOfSites` slot in a `parameterOptions` object.

Description

Setter Method for the noOfSites slot in a parameterOptions object.

Usage

noOfSites(object) <- value

Arguments

`object`	`object` is a `parameterOptions` object.
`value`	`value` is a positive integer that will be assigned to the `noOfSites` slot.

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 a parameterOptions object with an updated value for the noOfSites 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. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples

# Loading data
data(ChIPanalyserData)

#Building data objects
GPP <- parameterOptions(noOfSites=0)
#Setting new Value for naturalLog
noOfSites(GPP) <- 8

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