reconcileFeatures {ChIPsim} | R Documentation |
The reconcileFeatures
functions provide a facility to post-process a list of features representing
a simulated experiment. reconcileFeatures
is an S3 generic, new functions can be added for additional
types of experiment. The current default is to call reconcileFeatures.SimulatedExperiment
which, if
called without further arguments, will simply return the feature list unchanged.
reconcileFeatures(features, ...) ## Default S3 method: reconcileFeatures(features, ...) ## S3 method for class 'SimulatedExperiment' reconcileFeatures(features, defaultValues=list(), ...) ## S3 method for class 'NucleosomePosition' reconcileFeatures(features, defaultMeanDist = 200, ...)
features |
List of simulated features. |
defaultValues |
Named list of default parameter values. The method for class |
defaultMeanDist |
Default value for the average distance between nucleosomes for nucleosome positioning experiments. |
... |
Further arguments to future functions. |
A list of features of the same class as features
.
Peter Humburg
set.seed(1) ## generate a (relatively short) sequence of nucleosome features features <- makeFeatures(length=1e6, ) ## check the total length of the features sum(sapply(features, "[[", "length")) ## 995020 ## reconcile features to ensure smooth transitions ## For experiments of class NucleosomePosition this ## also combines some features and introduces ## some overlap between them. features <- reconcileFeatures(features) ## check the total length of the features again sum(sapply(features, "[[", "length")) ## 984170