# Simulation of ChIP-seq experiments

## Documentation for package ‘ChIPsim’ version 1.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ChIPsim-package | Simulation of ChIP-seq experiments
bindDens2readDens | Convert a feature density into a read density
ChIPsim | Simulation of ChIP-seq experiments
decodeQuality | Conversion between numerical and ASCII representation of read qualities
defaultControl | Default parameters for simChIP
defaultErrorProb | Replacement probabilities for sequencing errors
defaultFunctions | Default functions for simChIP
defaultGenerator | Defaults for Feature Generator
defaultInit | Defaults for Feature Generator
defaultLastFeat | Defaults for Feature Generator
defaultTransition | Defaults for Feature Generator
encodeQuality | Conversion between numerical and ASCII representation of read qualities
extractQuality | Obtain read qualities from a Fastq file or ShortReadQ object
feat2dens | Convert a list of features into a feature density
featureDensity | Computing density for a given feature
featureDensity.FuzzyFeature | Computing density for a given feature
featureDensity.NFRFeature | Computing density for a given feature
featureDensity.ReversePhasedFeature | Computing density for a given feature
featureDensity.StableFeature | Computing density for a given feature
featureDensity.StablePhasedFeature | Computing density for a given feature
fuzzyFeature | Generating Features
makeFeatures | Generating a list of genomic features
nfrFeature | Generating Features
phasedFeature | Generating Features
placeFeatures | Generating and reconciling a feature sequence
pos2fastq | Convert read positions to fastq records
readError | Introduce errors into read sequence based on quality scores
readQualitySample | Sample read qualities from a list
readSequence | Convert read position into read sequence
reconcileFeatures | Post-processing of simulated features
reconcileFeatures.default | Post-processing of simulated features
reconcileFeatures.NucleosomePosition | Post-processing of simulated features
reconcileFeatures.SimulatedExperiment | Post-processing of simulated features
sampleReads | Sampling sequence read positions from a read density.
simChIP | Simulate ChIP-seq experiments
simpleNames | Generate unique read names
stableFeature | Generating Features
writeFASTQ | Write read sequences and qualities to a FASTQ formatted file
writeReads | Create fastq file from read positions