processingChIP {ChIPanalyser} | R Documentation

## 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 accesible 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 <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)

    ## Extracting ChIP scores at loci of interest

    ChIP<-processingChIP(profile=eveLocusChip, loci=eveLocus)

[Package ChIPanalyser version 1.12.0 Index]