R: Computing genome wide PWM scores.

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]