backgroundSignal<- {ChIPanalyser}R Documentation

Setter method for backgroundSignal slot in a occupancyProfileParameters

Description

Setter method for backgroundSignal slot in a occupancyProfileParameters

Usage

backgroundSignal(object)<-value

Arguments

object

object is an occupancyProfileParameters object.

value

value is the value to be assigned to the backgroundSignal slot in occupancyProfileParameters. 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 occupancyProfileParameters object.

Value

Returns a occupancyProfileParameters object with a new value assigned to the averageExpPWMScore 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 occupancyProfileParameters object
OPP <- occupancyProfileParameters()
# Setting new value for backgroundSignal
backgroundSignal(OPP) <- 0.2
# Viewing whole object with new updated value
OPP
#Viewing single value in object
backgroundSignal(OPP)


[Package ChIPanalyser version 1.2.0 Index]