| backgroundSignal {ChIPanalyser} | R Documentation |
backgroundSignal slot in a
occupancyProfileParameters object.
Extract or access the backgroundSignal slot in a
occupancyProfileParameters object.
backgroundSignal(object)
object |
|
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
occupancyProfileParameters object.
Returns a backgroundSignal of a
occupancyProfileParameters object.
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, 84–94.
# Building occupancyProfileParameters object OPP <- occupancyProfileParameters() #Viewing single value in object backgroundSignal(OPP)