PositionFrequencyMatrix {ChIPanalyser} | R Documentation

## Accessor method for the `PFM` slot in a `genomicProfiles` object

### Description

Accessor method for the `PFM` slot in a `genomicProfiles` object

### Usage

    PositionFrequencyMatrix(object)

### Arguments

`object` | `object` is a `genomicProfiles` object

### Details

After creating a `genomicProfiles` object, it is possible to access the Position Frequency Matrix slot. However this slot will be empty if the `genomicProfiles` object was built using directly a Position Weight Matrix. See `genomicProfiles`

### Value

Returns the Position Frequency Matrix (`PFM` slot) used to compute the `PositionWeightMatrix` in a `genomicProfiles` 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 genomicProfiles object
    GPP<-genomicProfiles(PFM=PFM,PFMFormat="raw")
    # Accessing Slot
    PositionFrequencyMatrix(GPP)

[Package ChIPanalyser version 1.14.0 Index]