computeGenomeWidePWMScore {ChIPanalyser} | R Documentation |
computeGenomeWidePWMScore
scores the entire genome with a
Position Weight Matrix.
It is possible to restrict the scoring of the genome to only Accessible DNA.
computeGenomeWidePWMScore(DNASequenceSet, genomicProfileParameters, DNAAccessibility = NULL, cores=1, verbose = TRUE)
DNASequenceSet |
|
genomicProfileParameters |
|
DNAAccessibility |
|
cores |
|
verbose |
|
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
.
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.
Patrick C.N. Martin <pm16057@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
#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 <-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)