PWMpseudocount {ChIPanalyser} | R Documentation

## Accessor Method for a `PWMpseudocount` slot in a `genomicProfileParameters`

### Description

Accessor Method for a `PWMpseudocount` slot in a `genomicProfileParameters`

### Usage

    PWMpseudocount(object)

### Arguments

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

### Details

In the context of Position Weight Matricies, the pseudocount is used to avoid 0 probabilities during the transformation of Position Frequency Matrix to a Position Probability Matrix and finally to a Postion Weight Matrix. It is essentially a sample correction that is added in the case of small sample size. The effect of the base pair to which a pseudocount was assigned will not influence the model nor will create mathematical issues such as infinities or zero division. Default is set at 1.

### Value

Returns the value assigned to a `PWMpseudocount` slot in a `genomicProfileParameters` 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 data objects
    GPP <- genomicProfileParameters(PFM=PFM, PWMpseudocount=0)
    #Accessing slot value
    PWMpseudocount(GPP)

[Package ChIPanalyser version 1.2.0 Index]