HiCDOCDataSet
.R/AllClasses.R
, R/AllGenerics.R
, R/methods.R
HiCDOCDataSet-parameters.Rd
Retrieves or sets parameters used for filtering, normalization, and prediciton of compartments.
defaultHiCDOCParameters parameters(object) parameters(object) <- value
object | |
---|---|
value | a named list containing the names and valued of the parameters to change (see Details). |
An object of class list
of length 7.
A HiCDOCDataSet
's parameters are automatically set to default
values retrieved from defaultHiCDOCParameters
. They are
accessed by filtering, normalization, and compartment detection functions.
If those functions are called with custom arguments, the object's
parameters are updated to record the actual parameters used. If the
object's parameters are customized before calling the functions, the
custom parameters will be used.
smallChromosomeThreshold
The minimum length (number of positions) for a chromosome to be
kept when filtering with filterSmallChromosomes
.
Defaults to
defaultHiCDOCParameters$smallChromosomeThreshold
= 100.
sparseReplicateThreshold
The minimum percentage of non-zero interactions for a chromosome
replicate to be kept when filtering with
filterSparseReplicates
. If a chromosome replicate's
percentage of non-zero interactions is lower than this value, it
is removed. Defaults to
defaultHiCDOCParameters$smallChromosomeThreshold
= 30
weakPositionThreshold
The minimum average interaction for a position to be kept when
filtering with filterWeakPositions
. If a position's
average interaction with the entire chromosome is lower than this
value in any of the replicates, it is removed from all replicates
and conditions. Defaults to
defaultHiCDOCParameters$smallChromosomeThreshold
= 1.
loessSampleSize
The number of positions used as a sample to estimate the effect
of distance on proportion of interactions when normalizing with
normalizeDistanceEffect
Defaults to
defaultHiCDOCParameters$loessSampleSize
= 20000.
kMeansDelta
The convergence stop criterion for the clustering when detecting
compartments with detectCompartments
. When the
centroids' distances between two iterations is lower than this
value, the clustering stops. Defaults to
defaultHiCDOCParameters$kMeansDelta
= 0.0001.
kMeansIterations
The maximum number of iterations during clustering when detecting
compartments with detectCompartments
. Defaults to
defaultHiCDOCParameters$kMeansIterations
= 50.
kMeansRestarts
The amount of times the clustering is restarted when detecting
compartments with detectCompartments
. For each
restart, the clustering iterates until convergence or reaching
the maximum number of iterations. The clustering that minimizes
inner-cluster variance is selected. Defaults to
defaultHiCDOCParameters$kMeansRestarts
= 20.
defaultHiCDOCParameters
: Provides default parameters, imported into a HiCDOCDataSet
upon
instantiation. The HiCDOCDataSet
parameters are then used for the
HiCDOC
pipeline.
parameters
: Retrieves the parameters used for filtering, normalization, and prediction of
compartments. See
filterSmallChromosomes
,
filterSparseReplicates
,
filterWeakPositions
,
normalizeDistanceEffect
, and
detectCompartments
,
for details on how these parameters are used.
parameters<-
: Sets the parameters used for filtering, normalization, and prediciton of
compartments. See
filterSmallChromosomes
,
filterSparseReplicates
,
filterWeakPositions
,
normalizeDistanceEffect
, and
detectCompartments
,
for details on how these parameters are used.
#> $smallChromosomeThreshold #> [1] 100 #> #> $sparseReplicateThreshold #> [1] 0.3 #> #> $weakPositionThreshold #> [1] 1 #> #> $loessSampleSize #> [1] 20000 #> #> $kMeansDelta #> [1] 1e-04 #> #> $kMeansIterations #> [1] 50 #> #> $kMeansRestarts #> [1] 20 #>