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" |