segmentPICS: 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.

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.

Examples

Run this code

# 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)