backgroundSignal<- {ChIPanalyser} | R Documentation |
backgroundSignal
slot in a
parameterOptions
Setter method for backgroundSignal
slot in a
parameterOptions
backgroundSignal(object)<-value
object |
|
value |
|
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, 84–94.
# 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)