# MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

## Documentation for package ‘mosaics’ version 2.4.1

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

## Help Pages

mosaics-package | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
bdBin-method | Class "MosaicsPeak"
BinData-class | Class "BinData"
chrID-method | Class "BinData"
constructBins | Construct bin-level ChIP-sep data from an aligned read file
coord-method | Class "BinData"
empFDR-method | Class "MosaicsPeak"
estimates | Extract estimates of the fitted MOSAiCS model
estimates-method | Class "MosaicsHMM"
estimates-method | Extract estimates of the fitted MOSAiCS model
export | Export peak calling results to text files
export-method | Export peak calling results to text files
gcContent-method | Class "BinData"
generateWig | Construct wiggle files from an aligned ChIP-sep read file
input-method | Class "BinData"
mappability-method | Class "BinData"
mosaics | MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)
mosaicsFit | Fit MOSAiCS model
MosaicsFit-class | Class "MosaicsFit"
mosaicsFit-method | Fit MOSAiCS model
mosaicsFitHMM | Fit MOSAiCS-HMM model
mosaicsFitHMM-method | Fit MOSAiCS-HMM model
MosaicsHMM-class | Class "MosaicsHMM"
mosaicsPeak | Call peaks using fitted MOSAiCS model
MosaicsPeak-class | Class "MosaicsPeak"
mosaicsPeak-method | Call peaks using fitted MOSAiCS model
mosaicsPeakHMM | Call broad peaks using fitted MOSAiCS-HMM model
mosaicsPeakHMM-method | Call broad peaks using fitted MOSAiCS-HMM model
mosaicsRunAll | Analyze ChIP-seq data using the MOSAiCS framework
plot-method | Class "BinData"
plot-method | Class "MosaicsFit"
plot-method | Class "MosaicsHMM"
print-method | Class "BinData"
print-method | Class "MosaicsFit"
print-method | Class "MosaicsHMM"
print-method | Class "MosaicsPeak"
readBins | Import bin-level ChIP-sep data
show-method | Class "BinData"
show-method | Class "MosaicsFit"
show-method | Class "MosaicsHMM"
show-method | Class "MosaicsPeak"
tagCount-method | Class "BinData"