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


[Up] [Top]

Documentation for package ‘mosaics’ version 1.6.0

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 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
mosaicsPeak Call peaks using fitted MOSAiCS model
MosaicsPeak-class Class "MosaicsPeak"
mosaicsPeak-method Call peaks using fitted MOSAiCS model
mosaicsRunAll Analyze ChIP-seq data using the MOSAiCS framework
plot-method Class "BinData"
plot-method Class "MosaicsFit"
print-method Class "BinData"
print-method Class "MosaicsFit"
print-method Class "MosaicsPeak"
readBins Import bin-level ChIP-sep data
show-method Class "BinData"
show-method Class "MosaicsFit"
show-method Class "MosaicsPeak"
tagCount-method Class "BinData"