strandRule<- {ChIPanalyser} | R Documentation

## Setter method for the `strandRule` slot in a `genomicProfileParameters` object.

### Description

Setter method for the `strandRule` slot in a `genomicProfileParameters` object.

### Usage

    strandRule(object) <- value

### Arguments

`object` | `object` is a `genomicProfileParameters` object
`value` | `value` is a character string and can be one of the following ‘mean’, ‘max’, ‘sum’. This will only apply if `whichstrand` is ‘+-’. Default set at ‘max’

### Details

When computing the PWM Scores and if `whichstrand` is set to ‘+-’, `strandRule` will determine how to handle both strands ( one of three options : ‘mean’, ‘max’, ‘sum’). If set to ‘mean’, the average PWM Score of both strand will be computed. If set to ‘max’, the highest PWM score between each strand will be selected and finally ‘sum’ will sum both score together. Default set at ‘max’

### Value

Returns a `genomicProfileParameters` object with an updated value for the `strandRule` 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
    GPP <- genomicProfileParameters(PFM=PFM, strandRule="max")
    #Setting New Value for strandRule
    strandRule(GPP) <- "mean"

[Package ChIPanalyser version 1.2.0 Index]