averageExpPWMScore {ChIPanalyser} | R Documentation

## Accessor for `averageExpPWMScore` slot in a `genomicProfileParameters` object.

### Description

Extract or Access `averageExpPWMScore` slot in a `genomicProfileParameters`

### Usage

    averageExpPWMScore(object)

### Arguments

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

### Details

As a general rule, `averageExpPWMScore` is computed and updated internally by `computeGenomeWidePWMScore`. Idealy, this slot should not be updated by user. The `averageExpPWMScore` is the sum of the exponential of every PWM score for a given DNA sequence and divided by the length of the said DNA sequence (`DNASequenceLength`). This can either be the full length sequence or only the accessible sequence (see `computeGenomeWidePWMScore`).

### Value

Returns the `averageExpPWMScore` of a `genomicProfileParameters` when computed.

### 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

    # Accessing Data
    data(ChIPanalyserData)
    # path to Position Frequency Matrix
    PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
    # Building genomicProfileParameters object
    GPP <- genomicProfileParameters(PFM=PFM)
    # Extracting AllSitesAboveThreshold slot
    averageExpPWMScore(GPP)

    ## Note this slot is now empty as nothing has yet been computed

[Package ChIPanalyser version 1.2.0 Index]