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

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Accessor method for the backgroundSignal slot in a parameterOptions object.

Description

Extract or access the backgroundSignal slot in a parameterOptions object.

Usage

backgroundSignal(object)

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 <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

Examples

# Building occupancyProfileParameters object
OPP <- parameterOptions()
#Viewing single value in object
backgroundSignal(OPP)

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.