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 |
minReads |
A |
minReadsInRegion |
A |
jitter |
A |
dataType |
A |
maxLregion |
A |
minLregion |
A |
An object of class segReadsList
containing the results for all
pre-processed regions.
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.
segReadsList
# 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)