chipSmooth {ChIPanalyser}R Documentation

Accessor methods for chipSmooth slot in a occupancyProfileParameters object.

Description

Access or Extract chipSmooth slot in a occupancyProfileParameters object.

Usage

chipSmooth(object)

Arguments

object

object is a occupancyProfileParameters object.

Details

When computing ChIP-seq like (computeChipProfile) profile from occupancy data (see computeOccupancy), the profiles are smoothed using a window of a given size. The default value is set at 250 base pairs. If chipSmooth is set to 0 then the profile will not be smoothed. We strongly encourage to set values when building a occupancyProfileParameters object.

Value

Returns the chipSmooth slot in an occupancyProfileParameters object.

Author(s)

Patrick C.N. Martin <pm16057@essex.ac.uk>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

Examples

# Building occupancyProfileParameters object
OPP <- occupancyProfileParameters()
# Accessing chipSd slot
chipSmooth(OPP)

[Package ChIPanalyser version 1.2.0 Index]