segmentPICS {PICS} | R Documentation |
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.
segmentPICS(data, dataC=NULL, map=NULL, minReads=2, minReadsInRegion=3, jitter=FALSE, dataType="TF", maxLregion=0, minLregion=100)
data |
A |
dataC |
A |
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. |
An object of class segReadsList
containing the results for all regions pre-processed.
Xuekui Zhang, Arnaud Droit <arnaud.droit@crchuq.ualaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>
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.
# 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)