Simulation of ChIP-seq experiments

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Documentation for package ‘ChIPsim’ version 1.60.0

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

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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