segmentPICS {PICS} | R Documentation

## Segment the genome into candidate regions

### Description

Pre-process bidirectional aligned reads data from a single ChIP-Seq experiment to detect candidate regions with a minimum number of forward and reverse reads. These candidate regions will then be processed by PICS.

### Usage

    	segmentPICS(data, dataC=NULL, map=NULL, minReads=2, minReadsInRegion=3,
        jitter=FALSE, dataType="TF", maxLregion=0, minLregion=100)

### Arguments

`data` | A `linkS4class{GRanges}` object containing the IP reads. See details for more information on how to set up the data.
`dataC` | A `linkS4class{GRanges}` object containing the control reads. Set to NULL by default, i.e. no control.
`map` | A ‘RangedData’ object containing the mappability profiles. Set to NULL by default, i.e. no profiles.
`minReads` | The minimum number of F/R reads to be present in the sliding window.
`minReadsInRegion` | The minimum number of F/R reads to be present in the region.
`jitter` | A logical value stating whether some noise should be added to the read locations. This is recommended if the read positions have lots of duplicates.
`dataType` | Type of experiment. "TF" or "H".
`maxLregion` | The maximum length.
`minLregion` | The minimum length.

### Value

An object of class `segReadsList` containing the results for all regions pre-processed.

### 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.

### See Also

`segReadsList`

### Examples

    # Read data
    path<-system.file("extdata",package="PICS")
    ## Note that the col name for the chromosome needs to be space and not chr
    dataIP<-read.table(file.path(path,"Treatment_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
    dataIP<-as(dataIP,"GRanges")

    dataCont<-read.table(file.path(path,"Input_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
    dataCont<-as(dataCont,"GRanges")

    map<-read.table(file.path(path,"mapProfileShort"),header=TRUE,colClasses=c("factor","integer","integer","NULL"))
    map<-as(map,"GRanges")
    seg<-segmentPICS(dataIP, dataC=dataCont, map=map, minReads=1)

[Package PICS version 2.28.0 Index]