segmentPICS: Segment the genome into candidate regions
In PICS: Probabilistic inference of ChIP-seq

Description Usage Arguments Value References See Also Examples

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 `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 `GRanges` object containing the mappability profiles. Set to NULL by default, i.e. no profiles.
`minReads`	A `numeric`. The minimum number of F/R reads to be present in the sliding window.
`minReadsInRegion`	A `numeric`. 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`	A `character`. Type of experiment. "TF" or "H".
`maxLregion`	A `numeric`. The maximum length.
`minLregion`	A `numeric`. The minimum length.

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)