backgroundSignal_-: Setter method for 'backgroundSignal' slot in a...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Description Usage Arguments Details Value Author(s) References Examples

Setter method for backgroundSignal slot in a parameterOptions

1	backgroundSignal(object)<-value

`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.

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.

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

Patrick C.N. Martin <pm16057@essex.ac.uk>

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84<e2><80><93>94.

# 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)