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

PWMThreshold<-

R Documentation

Setter Method for the `PWMThreshold` slot in a `parameterOptions` object

Description

Setter Method for the PWMThreshold slot in a parameterOptions object

Usage

PWMThreshold(object) <- value

Arguments

`object`	`object` is a `parameterOptions` object
`value`	`value` is a numeric value (between 0 and 1) to be assigned to the `PWMThreshold` slot in `parameterOptions` object. Default is set at 0.7

Details

The computePWMScore function requires a so-called PWM Threshold. This threshold represents the Threshold at which PWM Score should be selected. The PWMThreshold is a positive numeric value (between 0 and 1. If set at 0, all sites will be selected. If set at 0.7 (Default value), then 70 % of PWM Score (and by extension binding sites) will be IGNORED. The top 30 % will be selected.

Value

Returns parameterOptions objetc with an updated value for the PWMThreshold slot

Author(s)

Patrick C. N. Martin <pm16057@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(PWMThreshold=0.7)
#Setting Value for new PWMThreshold
PWMThreshold(GPP) <- 0.8

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