backgroundSignal: Accessor method for the 'backgroundSignal' slot in a...

Description Usage Arguments Details Value Author(s) References Examples

Description

Extract or access the backgroundSignal slot in a parameterOptions object.

Usage

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Arguments

object

object is an parameterOptions

Details

Default Value: 0

When computing computeOccupancy, a ChIP-seq background signal is used to scale Occupancy by considering both a backgroundSignal and a maxSignal. The backgroundSignal is also used to nomalise occupancies against maxOccupancy. The backgroundSignal usually comes from experimental data and is provided by user. As a general rule, if ChIP-seq data is available and will be used in computeChIPProfile , profileAccuracyEstimate or plotOccupancyProfile, it is advised to use the backgroundSignal from this data. We strongly encourage to set values when building a parameterOptions object.

Value

Returns a backgroundSignal of a 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 occupancyProfileParameters object
OPP <- parameterOptions()
#Viewing single value in object
backgroundSignal(OPP)

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