mosaics (version 2.10.0)

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

Description

This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.

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Version

2.10.0

License

GPL (>= 2)

Maintainer

Dongjun Chung

Last Published

February 15th, 2017

Functions in mosaics (2.10.0)

adjustBoundary

Adjust boundaries of peak regions

MosaicsFitEst-class

Class "MosaicsFitEst"

MosaicsHMM-class

Class "MosaicsHMM"

constructBins

Construct bin-level ChIP-sep data from an aligned read file

generateWig

Construct wiggle files from an aligned ChIP-sep read file

extractReads

Load read-level data and extract reads corresponding to each peak region

Find a summit for each peak region

export

Export peak calling results to text files

mosaicsRunAll

Analyze ChIP-seq data using the MOSAiCS framework

mosaics-internal

Internal mosaics objects

MosaicsFitParam-class

Class "MosaicsFitParam"

MosaicsFit-class

Class "MosaicsFit"

estimates

Extract estimates of the fitted MOSAiCS model

MosaicsPeak-class

Class "MosaicsPeak"

mosaicsFitHMM

Fit MOSAiCS-HMM model

TagData-class

Class "TagData"

mosaicsPeakHMM

Call broad peaks using fitted MOSAiCS-HMM model

MosaicsPeakParam-class

Class "MosaicsPeakParam"

mosaics-package

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

mosaicsPeak

Call peaks using fitted MOSAiCS model

filterPeak

Filter out potentially false positive peaks

readBins

Import bin-level ChIP-sep data