BinData-class           Class "BinData"
MosaicsFit-class        Class "MosaicsFit"
MosaicsFitEst-class     Class "MosaicsFitEst"
MosaicsFitParam-class   Class "MosaicsFitParam"
MosaicsHMM-class        Class "MosaicsHMM"
MosaicsPeak-class       Class "MosaicsPeak"
MosaicsPeakParam-class
                        Class "MosaicsPeakParam"
TagData-class           Class "TagData"
adjustBoundary          Adjust boundaries of peak regions
constructBins           Construct bin-level ChIP-sep data from an
                        aligned read file
estimates               Extract estimates of the fitted MOSAiCS model
export                  Export peak calling results to text files
extractReads            Load read-level data and extract reads
                        corresponding to each peak region
filterPeak              Filter out potentially false positive peaks
findSummit              Find a summit for each peak region
generateWig             Construct wiggle files from an aligned ChIP-sep
                        read file
mosaics-package         MOSAiCS (MOdel-based one and two Sample
                        Analysis and Inference for ChIP-Seq)
mosaicsFit              Fit MOSAiCS model
mosaicsFitHMM           Fit MOSAiCS-HMM model
mosaicsPeak             Call peaks using fitted MOSAiCS model
mosaicsPeakHMM          Call broad peaks using fitted MOSAiCS-HMM model
mosaicsRunAll           Analyze ChIP-seq data using the MOSAiCS
                        framework
readBins                Import bin-level ChIP-sep data
