chipSmooth: Accessor methods for 'chipSmooth' slot in a...

Description Usage Arguments Details Value Author(s) References Examples

Description

Access or Extract chipSmooth slot in a parameterOptions object.

Usage

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chipSmooth(object)

Arguments

object

object is a parameterOptions 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 parameterOptions object.

Value

Returns the chipSmooth slot in an parameterOptions 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

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

patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.