computeGenomeWidePWMScore {ChIPanalyser} | R Documentation

## Computing genome wide PWM scores.

### Description

`computeGenomeWidePWMScore` scores the entire genome with a Position Weight Matrix. It is possible to restrict the scoring of the genome to only Accessible DNA.

### Usage

    computeGenomeWidePWMScore(DNASequenceSet, genomicProfileParameters,
        DNAAccessibility = NULL, cores=1, verbose = TRUE)

### Arguments

`DNASequenceSet` | `DNASequenceSet` is a `BSgenome` or a `DNAStringSet`. The DNASequenceSet is the sequence of the organism of interest. For a question of ease, it is advised to use a `DNAStringSet`
`genomicProfileParameters` | `genomicProfileParameters` is a `genomicProfileParameters` object. This object contains parameters needed to compute `computeGenomeWidePWMScore`. GenomicProfileParameters also contain the Position Weight Matrix. See `genomicProfileParameters` for more information.
`DNAAccessibility` | `DNAAccessibility` is a `GRanges` object containing Accessible DNA. If provided, the score will be score only on accesible DNA instead of genome wide.
`cores` | `cores` is the number of cores that will be used to compute Genome Wide PWM Scores.
`verbose` | `verbose` is a logical value. If TRUE, progress messages will be displayed in console. If FALSE, no progress message will be displayed.

### Details

After creating a `genomicProfileParameters` object, the genome can be scored in order to extract information required for further analysis. These values will be `maxPWMScore`, `minPWMScore`, `averageExpPWMScore` and finally `DNASequenceLength`. These values will be used in `computePWMScore`.

### Value

Returns a `genomicProfileParameters` object. This object will contain updated value for certain slots `maxPWMScore`, `minPWMScore`, `averageExpPWMScore` and finally `DNASequenceLength`. It should be mentioned that certain slot will remain empty as they will be computed in other functions.

### 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

    #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)){
        source("https://bioconductor.org/biocLite.R")
        biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
        }
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    DNASequenceSet <-DNAStringSet(BSgenome.Dmelanogaster.UCSC.dm3[["chr2R"]])
    names(DNASequenceSet) <- "chr2R"

    # Building genomicProfileParameters object
    GPP <- genomicProfileParameters(PFM=PFM, BPFrequency=DNASequenceSet)

    # Computing Genome Wide
    GenomeWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet,
        genomicProfileParameters = GPP)
    # Computing Genome wide with DNA accessibility
    GenomeWide <- computeGenomeWidePWMScore(DNASequenceSet = DNASequenceSet,
        genomicProfileParameters = GPP, DNAAccessibility = Access,
        GenomeWide = FALSE)

[Package ChIPanalyser version 1.2.0 Index]