makeRangedDataOutput {PICS} | R Documentation

## Create a RangedData object from a PICS output

### Description

Create a list of ‘RangedData’ objects from a ‘pics’ object. The resulting RangedData object can then be analyzed with the ‘IRanges’ packages and/or exported to bed/wig files with the ‘rtracklayer’ package.

### Usage

    makeRangedDataOutput(obj, type="fixed", filter=list(delta=c(0,Inf),se=c(0,Inf),sigmaSqF=c(0,Inf),sigmaSqR=c(0,Inf),score=c(0,Inf)),length=100)

### Arguments

`obj` | An object of class ‘picsList’ as returned by ‘PICS’ when running it on the IP/Control data.
`type` | The type of intervals to be created. The different types are ‘bed’, ‘wig’, ‘ci’ and ‘fixed’. See details for more info.
`filter` | A list of filters to be used before computing the FDR. By default all regions are included, see details for more info on how to specify the filters.
`length` | The length to be used for the fixed type ‘RangedData’, see details.

### Details

‘bed’ will generate intervals from the forward peak max to the reverse peak max. ‘wig’ will generate a density profile for the forward and reverse reads. ‘bed’ and ‘wig’ types should be used to be exported to wig/bed files to be used with the UCSC genome browser. ‘ci’ corresponds to the binding site estimates +/-3*se, while ‘fixed’ corresponds to the binding site estimates +/-3*length. ‘bed’ and ‘wig’ files can be exported using the ‘export’ function fo the ‘rtracklayer’ package.

### Value

An object of type ‘RangedData’.

### Author(s)

Xuekui Zhang, Arnaud Droit <arnaud.droit@crchuq.ualaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>

### References

X. Zhang, G. Robertson, M. Krzywinski, K. Ning, A. Droit, S. Jones, and R. Gottardo, “PICS: Probabilistic Inference for ChIP-seq” arXiv, 0903.3206, 2009. To appear in Biometrics.

### See Also

export

### Examples

    ## Not run:
      rdBed<-makeRangedDataOutput(pics,type="bed",filter=list(delta=c(50,Inf),se=c(0,50),sigmaSqF=c(0,22500),sigmaSqR=c(0,22500),score=c(10,Inf)))
      export(rbBed,"myfile.bed")
      rdBed<-makeRangedDataOutput(pics,type="wig",filter=list(delta=c(50,Inf),se=c(0,50),sigmaSqF=c(0,22500),sigmaSqR=c(0,22500),score=c(10,Inf)))
      export(rbBed,"myfile.wig")
    ## End(Not run)

[Package PICS version 2.28.0 Index]