PICS (version 2.16.0)

makeRangedDataOutput: 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.

Value

An object of type `RangedData'.

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.

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)