processingChIP: Pre-processing ChIP-seq data

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Pre-processing ChIP-seq data

Description

processingChIP will process and extract ChIP scores at a set of loci of interest.

Usage

processingChIP(profile,loci=NULL,reduce=NULL,
     peaks=NULL,chromatinState=NULL,parameterOptions=NULL,
     cores=1)

Arguments

profile	profile is a path to a UCSC format file, a GRanges or data frame. The input data should contain 4 columns:chromosome, start , end and score.
loci	loci is GRanges describing the loci at which ChIP scores should be extracted. If NULL, a set of Loci will extracted from profile. The data provided will then be split into bins of width equal to lociWidth (Default 20kbp) Default=NULL
reduce	reduce is a the top regions to select based on the mean ChIP score. If peaks are provided, regions overlappling with known peaks will be selected based on highest ChIP score. If NULL, all regions will be considered. Default=NULL
parameterOptions	parameterOptions is an parameterOptions object containing chip Parameters to be parsed for ChIP score extraction. If NULL, parameterOptions will be built internally with default ChIP extraction parameters (see chipSmooth, chipSd and chipMean) Default=NULL
peaks	peaks is a path to UCSC format file or a GRanges object containing location of ChIP peaks. Default=NULL
chromatinState	chromatinState is a GRanges containing Accessible DNA or chromatin States If provided, regions will be selected only if they contain accessible DNA. Default=NULL
cores	cores is the number of cores used to extract ChIP scores. Default = 1

Details

When using computeOptimal, it is required to supply real ChIP data in order to have a point of comparison. The corralation and MSE Scores are computed based of how well the model fits biological data. processingChIP will extract this data from ChIP data at loci of interest. When using the reduce option, this function will only select the top regions based on peak height or mean ChIP score. processingChIP will also extract maxSignal and backgroundSignal from ChIP data and parse it to an parameterOptions object.

Value

Returns a ChIPScore object containing extracted (and normalised) ChIP scores, the loci of interest and newly extracted Parameters(e.g. maxSignal)

Author(s)

Patrick C.N. Martin <[e-mail]>

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

#Data extraction
data(ChIPanalyserData)

## Extracting ChIP scores at loci of interest

ChIP<-processingChIP(profile=chip, loci=top)

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