segmentPICS {PICS} | R Documentation

## 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 `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.

### Value

An object of class `segReadsList` containing the results for all pre-processed regions.

### 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.

### See Also

segReadsList

### Examples

    # 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)

[Package PICS version 2.38.0 Index]