Description Usage Arguments Details Value Author(s) References Examples
Extract or access the backgroundSignal
slot in a
parameterOptions
object.
1 | 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
parameterOptions
object.
Returns a backgroundSignal
of a
parameterOptions
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<e2><80><93>94.
1 2 3 4 | # Building occupancyProfileParameters object
OPP <- parameterOptions()
#Viewing single value in object
backgroundSignal(OPP)
|
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