computeGenomeWideScores: Computing Genome Wide scores
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

computeGenomeWideScores

R Documentation

Computing Genome Wide scores

Description

computeGenomeWideScores compute the max and min PWM score over the entire genome.

Usage

computeGenomeWideScores(genomicProfiles, DNASequenceSet, chromatinState = NULL, parameterOptions = NULL, cores = 1, verbose = TRUE)

Arguments

`genomicProfiles`	`genomicProfiles` is a `genomicProfiles` object containing the PFM, PWM of interest.
`DNASequenceSet`	`DNASequenceSet` is a BSgenome or DNAStringSet containing the sequence of the organism of interest.
`chromatinState`	`chromatinState` is a GRanges object containing the chromatin States. This can either represent regions of accessible DNA or Chromatin state affinities.
`parameterOptions`	`parameterOptions` is a `parameterOptions` object containing parameters that you wish to change. The genomicProfiles object will be updated using the values assigned to `parameterOptions`
`cores`	`cores` is the number or cores that will be used (Numeric value - Default = 1 )
`verbose`	`verbose` is a logical value that will determine if internal progress message will be printed.

Details

computeGenomeWideScores function computes PWM scores over the entire genome (or accessible Genome if chromatin State are provided ). Genome wide scores are used to determine the maximum and minimum PWM score as well as the average exponential score. These scores will in turn be used to determine which score are above the PWM theshold. The average exponential score is an integrale part of the equation used to compute Occupancy. Using defualt settings, ChIPanalyser will only compute occupancy on the top 70% of PWM scores. This threshold can be changed. See PWMThreshold

Value

Returns a genomicsProfiles object with updated values for max score, min score and averageExpPWMScore.

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. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples


  
  if(!require("BSgenome.Dmelanogaster.UCSC.dm6", character.only = TRUE)){
      if (!requireNamespace("BiocManager", quietly=TRUE))
          install.packages("BiocManager")
      BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm6")
      }
  library(BSgenome.Dmelanogaster.UCSC.dm6)
  DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm6)
  # Building genomicProfiles object
  GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR", BPFrequency=DNASequenceSet)


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

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.