Simulation of ChIP-seq experiments


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Documentation for package ‘ChIPsim’ version 1.60.0

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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