backgroundSignal_-: Setter method for 'backgroundSignal' slot in a...

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

Setter method for backgroundSignal slot in a parameterOptions

Description

Setter method for backgroundSignal slot in a parameterOptions

Usage

backgroundSignal(object)<-value

Arguments

object	object is an parameterOptions object.
value	value is the value to be assigned to the backgroundSignal slot in parameterOptions. backgroundSignal should be a positive value. Defualt value is 0.

Details

Defualt 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 to 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 parameterOptions object with a new value assigned to the backgroundSignal slot.

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()
# Setting new value for backgroundSignal
backgroundSignal(OPP) <- 0.2
# Viewing whole object with new updated value
OPP
#Viewing single value in object
backgroundSignal(OPP)

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