PFMFormat {ChIPanalyser} | R Documentation

## Accesor method for the `PFMFormat` slot in a `genomicProfileParameters` object

### Description

Accesor method for the `PFMFormat` slot in a `genomicProfileParameters` object

### Usage

    PFMFormat(object)

### Arguments

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

### Details

If loading a `PositionFrequencyMatrix` from a file, the format of the file should be specified. Default is raw. Please keep in mind that this argument is used when parsing the `PositionFrequencyMatrix` file. IF this argument is changed after building the `genomicProfileParameters` with a PositionFrequencyMatrix file, this will not influence the parsing of the file. `PFMFormat` can be one of the following: "raw","transfac","JASPAR" or "sequences"

### Value

Returns the value assigned to the `PFMFormat` slot a `genomicProfileParameters`

### 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
    #### THIS IS THE PREFFERED METHOD FOR SETTING PFMFormat
    GPP <- genomicProfileParameters(PFM=PFM,PFMFormat="raw")
    #Setting New value for PFMFormat
    PFMFormat(GPP)

[Package ChIPanalyser version 1.2.0 Index]