minPWMScore {ChIPanalyser} | R Documentation

## Accessor method the `minPWMScore` slot in a `genomicProfiles` object

### Description

Accessor method the `minPWMScore` slot in a `genomicProfiles` object

### Usage

    minPWMScore(object)

### Arguments

`object` | `object` is a `genomicProfiles` object.

### Details

`minPWMScore` can be described as the lowest PWM score computed at a genome wide scale. Although it is possible to assigne a value to `minPWMScore`, we strongly advise to use the value computed and assigned internally. This value is computed in the `computeGenomeWideScores` function.

### Value

Returns the value assigned to the `minPWMScore` slot in a `genomicProfiles` object.

### Author(s)

Patrick C. N. Martin <p.martin@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

    #Data extraction
    data(ChIPanalyserData)
    # path to Position Frequency Matrix
    PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
    #As an example of genome, this example will run on the Drosophila genome

    if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
        if (!requireNamespace("BiocManager", quietly=TRUE))
            install.packages("BiocManager")
        BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
    }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
    #Building data objects
    GPP <- genomicProfiles(PFM=PFM,PFMFormat="raw")

    # Computing Genome Wide
    GenomceWide <- computeGenomeWideScores(DNASequenceSet = DNASequenceSet,
        genomicProfiles = GPP)
    minPWMScore(GenomceWide)

    ## If used before computeGenomeWidePWMScore, will return NULL

[Package ChIPanalyser version 1.14.0 Index]