segmentPING: 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.

A logical. Set to TRUE for Paired-End sequencing data.

islandDepth, min_cut, max_cut, maxReadsWidth

Parameters used for paired-end sequencing data segmentation.

Value

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

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.

Examples

Run this code

# 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)