chipSmooth<- {ChIPanalyser}R Documentation

Setter method for chipSmooth slot in parameterOptions object.

Description

Setter method for chipSmooth slot in parameterOptions object.

Usage

chipSmooth(object) <- value

Arguments

object

object is a parameterOptions object.

value

value is the positive numeric value to be assigned to the chipSmooth slot in parameterOptions Default value is 250 base pairs.

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 parameterOptions object.

Value

Returns a parameterOptions object with an updated value for chipSmooth slot.

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 parameterOptions object
OPP <- parameterOptions()
# Setting new value for chipSd slot
chipSmooth(OPP) <-  250
[Package ChIPanalyser version 1.9.1 Index]