reconcileFeatures: Post-processing of simulated features

In ChIPsim: Simulation of ChIP-seq experiments

Description

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.

Usage

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, ...)

Arguments

features	List of simulated features.
defaultValues	Named list of default parameter values. The method for class SimulatedExperiment ensures that all features have at least the parameters listed in defaultValues, adding them where necessary.
defaultMeanDist	Default value for the average distance between nucleosomes for nucleosome positioning experiments.
...	Further arguments to future functions.

Value

A list of features of the same class as features.

Author(s)

Peter Humburg

See Also

makeFeatures, placeFeatures

Examples

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

ChIPsim documentation built on Nov. 8, 2020, 8:09 p.m.