PFMFormat<- {ChIPanalyser} | R Documentation

## Setter method for the `PFMFormat` slot in a `genomicProfiles` object

### Description

Setter method for the `PFMFormat` slot in a `genomicProfiles` object

### Usage

    PFMFormat(object) <- value

### Arguments

`object` | `object` is a `genomicProfiles` object
`value` | `value` is character string of one of the following: "raw","transfac","JASPAR" or "sequences". If loading a `PositionFrequencyMatrix` from a file, the format of the file should specified. Default is raw.

### 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 `genomicProfiles` with a PositionFrequencyMatrix file, this will not influence the parsing of the file.

### Value

Returns a `genomicProfiles` object with an updated value for the `PFMFormat` slot.

### 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 <- genomicProfiles(PFM=PFM,PFMFormat="raw")
    #Setting New value for PFMFormat
    PFMFormat(GPP) <- "raw"

[Package ChIPanalyser version 1.12.0 Index]