segReadsGeneric: Perform genome segmentation depending

Description Usage Arguments

View source: R/segReadsGeneric.R

Description

Perform genome segmentation depending

Usage

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segReadsGeneric(
  data,
  dataC = NULL,
  map = NULL,
  minReads = 2,
  minReadsInRegion = 3,
  jitter = FALSE,
  maxLregion = 0,
  minLregion = 100,
  step = 20,
  width = 250,
  package = "PICS"
)

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.

maxLregion

A numeric. The maximum length.

minLregion

A numeric. The minimum length.

step

A numeric. The increment of the sliding window.

width

A numeric. The width of the region.

package

A character. "PICS" or "PING"


PICS documentation built on Nov. 8, 2020, 8:21 p.m.