occupancyProfileParameters {ChIPanalyser} | R Documentation |
occupancyProfileParameters
is a parameter storage object.
Similarly to genomicProfileParameters
,
this object serves the purpose of handling the set of parameters
needed when using certain functions.
occupancyProfileParameters(ploidy = 2 , boundMolecules = 1000 , backgroundSignal = 0 , maxSignal = 1 , chipMean = 150 , chipSd = 150 , chipSmooth = 250 , stepSize = 10 , removeBackground = 0 )
ploidy |
|
boundMolecules |
|
backgroundSignal |
|
maxSignal |
|
chipMean |
|
chipSd |
|
chipSmooth |
|
stepSize |
|
removeBackground |
|
The purpose of this occupancyProfileParameters
object is to store
paramters used duing certin of the functions available in ChIPanalyser
.
As opposed to genomicProfileParameters
, this object is not required
for a function to run as all paramters have default values ( the object will
be created internally as default values will be used - This also means that
no argument is required for this object to be built). However, it is
strongly advised to set these parameters to increase the goodness of fit
between the predicted Profiles and the real ChIP-seq profiles. As an example,
maxSignal
is the maximum signal of the real ChIP-seq data,
this signal will depend on the data being used thus should be tuned to
opimise the model.
Default values are set at:
ploidy = 2
boundMolecules = 1000
backgroundSignal = 0
maxSignal = 1
chipMean = 150
chipSd = 150
chipSmooth = 250
stepSize = 10
removeBackground = 0
Returns 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.
occupancyProfileParameters-class
genomicProfileParameters
genomicProfileParameters-class
OPP <- occupancyProfileParameters() # OR OPP <- occupancyProfileParameters(ploidy=2, boundMolecules=5000,backgroundSignal=0)