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

## Documentation for package ‘mosaics’ version 2.28.0

- 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)
adjustBoundary | Adjust boundaries of peak regions
adjustBoundary-method | Adjust boundaries of peak regions
bdBin | Class "MosaicsPeak"
bdBin-method | Class "MosaicsPeak"
BinData-class | Class "BinData"
chrID | Class "BinData"
chrID-method | Class "BinData"
constructBins | Construct bin-level ChIP-sep data from an aligned read file
coord | Class "BinData"
coord-method | Class "BinData"
empFDR | Class "MosaicsPeak"
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
extractReads | Load read-level data and extract reads corresponding to each peak region
extractReads-method | Load read-level data and extract reads corresponding to each peak region
filterPeak | Filter out potentially false positive peaks
filterPeak-method | Filter out potentially false positive peaks
findSummit | Find a summit for each peak region
findSummit-method | Find a summit for each peak region
gcContent | Class "BinData"
gcContent-method | Class "BinData"
generateWig | Construct wiggle files from an aligned ChIP-sep read file
input | Class "BinData"
input-method | Class "BinData"
mappability | 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
MosaicsFitEst-class | Class "MosaicsFitEst"
mosaicsFitHMM | Fit MOSAiCS-HMM model
mosaicsFitHMM-method | Fit MOSAiCS-HMM model
MosaicsFitParam-class | Class "MosaicsFitParam"
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
MosaicsPeakParam-class | Class "MosaicsPeakParam"
mosaicsRunAll | Analyze ChIP-seq data using the MOSAiCS framework
plot-method | Class "BinData"
plot-method | Class "MosaicsFit"
plot-method | Class "MosaicsHMM"
plot-method | Class "MosaicsPeak"
postProb | Class "MosaicsPeak"
postProb-method | Class "MosaicsPeak"
print-method | Class "BinData"
print-method | Class "MosaicsFit"
print-method | Class "MosaicsHMM"
print-method | Class "MosaicsPeak"
read | Class "MosaicsPeak"
read-method | Class "MosaicsPeak"
readBins | Import bin-level ChIP-sep data
readCoverage | Class "MosaicsPeak"
readCoverage-method | Class "MosaicsPeak"
seqDepth | Class "BinData"
seqDepth-method | Class "BinData"
seqDepth-method | Class "MosaicsFit"
seqDepth-method | Class "MosaicsHMM"
seqDepth-method | Class "MosaicsPeak"
show-method | Class "BinData"
show-method | Class "MosaicsFit"
show-method | Class "MosaicsHMM"
show-method | Class "MosaicsPeak"
tagCount | Class "BinData"
tagCount-method | Class "BinData"
TagData-class | Class "TagData"