segmentPING {PING} | R Documentation

## Segment the genome into candidate regions

### Description

Pre-process bidirectional aligned reads data to detect candidate regions with a minimum number of forward and reverse reads. These candidate regions will then be processed by PING.

### Usage

    	segmentPING(data, dataC=NULL, map=NULL, minReads=2, minReadsInRegion=3,
        jitter=FALSE, maxLregion=1200, minLregion=80, step=NULL, width=NULL,
        islandDepth=3, min_cut=50, max_cut=1000, maxReadsWidth=500, PE=FALSE)

### Arguments

`data` | A `GRanges` object containing the IP reads. See details for more information on how to set up the data.
`dataC` | A `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.
`step` | An `integer`. The step size for the sliding window.
`width` | An `integer`. The size of the sliding window.

`maxLregion` | The maximum length.
`minLregion` | The minimum length.
`PE` | A `logical`. Set to TRUE for Paired-End sequencing data.
`islandDepth, min_cut, max_cut, maxReadsWidth` | Parameters used for paired-end sequencing data segmentation.

islandDepth

  An `integer`. The minimum number of reads to cover a candidate region.

min_cut

  An `integer`. The minimum length of a candidate region.

max_cut

  An `integer`. The maximum length of a candidate region.

maxReadsWidth

  An `integer`. Reads with width superior to this limit will be removed from the data.

### 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

Xuekui Zhang, Gordon Robertson, Sangsoon Woo, Brad G. Hoffman, and Raphael Gottardo, "Probabilistic Inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data" PlosONE.

### See Also

`segReadsList`

### Examples

    # Read data
    path<-system.file("extdata",package="PING")
    dataIP<-read.table(file.path(path,"GSM351492_R4_chr1.bed"),header=TRUE)
    dataIP<-as(dataIP,"GRanges")
    seg<-segmentPING(dataIP,  minReads=NULL, maxLregion=1200,minLregion=80, jitter=TRUE)

[Package PING version 2.30.0 Index]