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

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Documentation for package ‘mosaics’ version 2.44.0

• 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"