PWMThreshold {ChIPanalyser} | R Documentation

## Accessor method for the `PWMThreshold` slot in a `genomicProfileParameters` object

### Description

Accessor method for the `PWMThreshold` slot in a `genomicProfileParameters` object

### Usage

    PWMThreshold(object)

### Arguments

`object` | `object` is a `genomicProfileParameters` object

### 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 the value assinged to the `PWMThreshold` slot in a `genomicProfileParameters` object

### 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.

### Examples

    # Loading data
    data(ChIPanalyserData)
    #Loading PFM files
    PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
    #Building data objects
    GPP <- genomicProfileParameters(PFM=PFM, PWMThreshold=0.7)
    #Accessing Value for  PWMThreshold
    PWMThreshold(GPP)

[Package ChIPanalyser version 1.2.0 Index]