genomicProfileParameters {ChIPanalyser}R Documentation

Genomic Profile Parameter Object

Description

genomicProfileParameter is a data/parameter storing object. The main purpose of this object is to store parameters neccessary for further computation but also store results. This makes parsing data and parameters easier between the different of functions available in ChIPanalyser.

Usage



genomicProfileParameters(PWM = NULL, PFM = NULL,PFMFormat="raw",
    ScalingFactorPWM = 1,
    PWMpseudocount = 1, noOfSites = 0, BPFrequency = rep(0.25, 4),
    naturalLog = FALSE, PWMThreshold = 0.7, strandRule = "max",
    whichstrand = "+-")

Arguments

PFM

PFM is a positon Frequency matrix. This matrix can either be supplied directly as a matrix (in the following form: 1 row for each base pair - ACTG in order - and a number of rows equal to the number of base pairs in the binding site) or can be supplied as path to a file containing the Position Frequency Matrix. At least ONE of either the PFM or PWM must be supplied. This is the minimum to build a genomicProfileParameters object. NOTE: Although the object will build, NO computation can be carried out without at least a PFM or a PWM.

PWM

PWM is a position weight matrix. This can be provided in matrix form (1 row for each base pair - ACTG in order - and a number of rows equal to the number of base pairs in the binding site). If a PFM is provided the PWM will be computed internally. NOTE: Although the object will build, NO computation can be carried out without at least a PFM or a PWM.

PFMFormat

PFMFormat is a character string describing the format of the file used (if any) in PositionFrequencyMatrix. ChIPanalyser handles most PFM formats thus this argument should take one of the following: raw, transfac, JASPAR or sequences.

ScalingFactorPWM

ScalingFactorPWM: A vector (or single value) contaning values for the ScalingFactorPWM (Also known as lambda).Default:1

PWMpseudocount

PWMpseudocount: A numeric value describing a PWMpseudocount for PWM computation. Default:1

BPFrequency

BPFrequency: Base Pair Frequency in the genome (if a DNA sequence is provided (as a DNAStringSet or BSgenome) , will be automatically computed internally). Default:c(0.25,0.25,0.25,0.25

naturalLog

naturalLog: A logical value describing if natural Log will be used to compute the PWM (if FALSE then log2 will be used). Default: TRUE

noOfSites

noOfSites: A Positive integer descibing number of sites (in base pair) should be used from the PFM to compute PWM. Default =0 (Full width of binding site will be used when set to 0)

PWMThreshold

PWMThreshold: Threshold at which PWM Score should be selected (only sites above threshold will be selected - between 0 and 1)

strandRule

strandRule: ‘mean’, ‘max’ or ‘sum’ will dertermine how strand should be handle for computing PWM Scores. Default : ‘max’

whichstrand

whichstrand: ‘+’,‘-’ or ‘+-’ on which strand should PWM Score be computed. Default: ‘+-’

Details

Most functions in ChIPanalyser require some form of a genomicProfileParameters object. It is required to build a genomicProfileParameters object before starting any computation. Most functions will return a genomicProfileParameters and thus this object should be parsed to the next function and so on. Most parameters are customisable and we strongly advise to do so. This can either be done directly (advised method) when building the genomicProfileParameters or by using setter methods. The former is advised as certain value are computed internally and require that parameters are set before hand ( e.g BPFrequency ). It is important to note that not all slots/parameters can be set by user. The value assinged to these slots are computed internally. For more information on this slots, see genomicProfileParameters-class. The following describes the default values and which slot are computed internally:

PWM = To be supplied by user

PFM = To be supplied by user

PFMFormat ="raw"

ScalingFactorPWM = 1

PWMpseudocount = 1

BPFrequency = c(0.25,0.25,0.25,0.25)

naturalLog = TRUE

noOfSites = 0

minPWMScore = Internally Computed

maxPWMScore = Internally Computed

PWMThreshold = 0.7

AllSitesAboveThreshold = Internally Computed

DNASequenceLength = Internally Computed (may still be provided by user see DNASequenceLength<-)

averageExpPWMScore = Internally Computed

strandRule = ‘max’

whichstrand = ‘+-’

NoAccess = Internally Computed

ZeroBackground = Internally Computed

Value

Returns a genomicProfileParameters 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.

See Also

genomicProfileParameters-class occupancyProfileParameters occupancyProfileParameters-class

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 genomicProfileParameters object
GPP <- genomicProfileParameters(PFM=PFM, ScalingFactorPWM=c(1,1.5,2),
    BPFrequency=DNASequenceSet)


[Package ChIPanalyser version 1.4.0 Index]