PositionWeightMatrix<- {ChIPanalyser} | R Documentation

## Setter Method for the `PositionWeightMatrix` slot in a `genomicProfileParameters` object

### Description

Setter Method for the `PositionWeightMatrix` slot in a `genomicProfileParameters` object

### Usage

    PositionWeightMatrix(object) <- value

### Arguments

`object` | `object` is a `genomicProfileParameters` object
`value` | `value` is a matrix in the form of a Position Weight Matrix.

### Details

If a Position Weight Matrix is readily available, it is possible to directly assign this matrix to the `PWM` slot. However, this is only possible if a `genomicProfileParameters` object has already been created. In that case, we advise to first create a `genomicProfileParameters` object. It should be noted that this Position Weight Matrix will be automatically computed from a Position Frequency Matrix. If no Position Frequency Matrix are available, then a Position Weight Matrix can be directly assigned to this slot.

### Value

Returns a `genomicProfileParameters` object with an updated value for the `PWM` 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

    #Building genomicProfileParameters object
    GPP <- genomicProfileParameters()
    #Setting PWM to PositionWeightMatrix slot
    PWM <- matrix(runif(32,-10,20), ncol=8)
    rownames(PWM) <- c("A","C","T","G")
    PositionWeightMatrix(GPP) <- PWM

[Package ChIPanalyser version 1.2.0 Index]