segmentPING {PING} | R Documentation |
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.
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)
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. |
step |
An |
width |
An |
maxLregion |
The maximum length. |
minLregion |
The minimum length. |
PE |
A |
islandDepth, min_cut, max_cut, maxReadsWidth |
Parameters used for paired-end sequencing data segmentation. |
An integer
. The minimum number of reads to cover a candidate region.
An integer
. The minimum length of a candidate region.
An integer
. The maximum length of a candidate region.
An integer
. Reads with width superior to this limit will be removed from the data.
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>
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.
# 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)