processingChIPseq {ChIPanalyser} | R Documentation

## Pre-processing ChIP-seq data from UCSC format file

### Description

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

### Usage

    processingChIPseq(profile,loci=NULL,reduce=NULL,
    occupancyProfileParameters=NULL,peaks=NULL,Access=NULL,cores=1)

### Arguments

`profile` | `profile` is a path to a UCSC format file, a GRanges or a data.frame containing ChIP scores. The input data frame should contain 4 columns: chromosome, start , end and score. This is also applicable for the GRanges format.
`loci` | `loci` is `GRanges` describing the loci at which ChIP scores should be extracted. If NULL, a set of Loci will extracted from `profile` based on chromosomes. However, we STRONGLY recommend to use a `GRanges` of loci of interest. 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
`occupancyProfileParameters` | `occupancyProfileParameters` is an `occupancyProfileParameters` object containing chip Parameters to be parsed for ChIP score extraction. If NULL, `occupancyProfileParameters` 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
`Access` | `Access` is a `GRanges` containing Accessible DNA. 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. `processingChIPseq` 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. `processingChIPseq` will also extract maxSignal and backgroundSignal from ChIP data and parse it to an `occupancyProfileParameters` object.

### Value

If using reduce, will return a list of two elements. The first element will contain a list with extracted ChIP data and a new set of top scoring loci loci. The second element will contain a `occupancyProfileParameters` object with maxSignal and backgroundSignal slot updated. If NOT using reduce, the first element will only contain ChIP score at loci of interest the second will still contain a `occupancyProfileParameters` object with maxSignal and backgroundSignal slot updated.

### 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<-processingChIPseq(profile=eveLocusChip, loci=eveLocus)

[Package ChIPanalyser version 1.2.0 Index]