AllSitesAboveThreshold {ChIPanalyser} | R Documentation

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

### Description

Extract or Access `AllSitesAboveThreshold` slot in `genomicProfileParameters` object.

### Usage

    AllSitesAboveThreshold(object)

### Arguments

`object` | `genomicProfileParameters` object.

### Details

As a general rule, `AllSitesAboveThreshold` is computed and updated internally in `computePWMScore`, `computeOccupancy`, `computeChipProfile`. Idealy, this slot should not be updated by user. There are three differenrent occurances of this slot. As a `GRanges`, `AllSitesAboveThreshold` represents the sites of one locus that are above `PWMThreshold`. As a `GRangesList`, `AllSitesAboveThreshold` represents the sites of multiple loci that are above `PWMThreshold`. As a `list`, `AllSitesAboveThreshold` represents a list of `GRanges` or `GRangesList` (as described above). When computing occupancy `computeOccupancy`, it is possible to use mutliple values of `ScalingFactorPWM` and `boundMolecules`. Each element in the list reprensent a combination of `ScalingFactorPWM` and `boundMolecules`. The specific combination of each element can be found by using `names` of `AllSitesAboveThreshold` or by using `ScalingFactorPWM` and `boundMolecules`.

### Value

Returns a `GRanges` , `GRangesList` or `list` containing containing sites with a Position Weight Matrix Score above a `PWMThreshold`.

### 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
    AllSitesAboveThreshold(GPP)

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

[Package ChIPanalyser version 1.2.0 Index]