PWMpseudocount<- {ChIPanalyser} | R Documentation

## Setter Method for the `pseudocount` slot in a `parameterOptions` object

### Description

Setter Method for the `pseudocount` slot in a `parameterOptions` object

### Usage

    PWMpseudocount(object) <- value

### Arguments

`object` | `object` is a `parameterOptions` object
`value` | `value` is a numeric value that will be assigned to the `pseudocount` slot. Defualt is set at 1

### 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.

### Value

Returns a `parameterOptions` object with an updated value for the `pseudocount` 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)

    #Building data objects
    GPP <- parameterOptions( PWMpseudocount=0)
    #Setting Value for new PWMpseudocount
    PWMpseudocount(GPP) <- 1

[Package ChIPanalyser version 1.12.0 Index]