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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mosaics")
AuthorDongjun Chung, Pei Fen Kuan, Rene Welch, Sunduz Keles
Bioconductor views Bioinformatics ChIPseq Genetics Sequencing Transcription
Date of publicationNone
MaintainerDongjun Chung <dongjun.chung@gmail.com>
LicenseGPL (>= 2)
Version2.14.0
http://groups.google.com/group/mosaics_user_group

View on Bioconductor

Functions

.adapGridMosaicsZ0_IO Man page
.adapGridMosaicsZ0_OS Man page
.adapGridMosaicsZ0_TS Man page
adjustBoundary Man page
adjustBoundary,MosaicsPeak-method Man page
bdBin Man page
bdBin,MosaicsPeak-method Man page
BinData-class Man page
.calcModelBIC Man page
.calcPN Man page
.calMDZ1_2S Man page
chrID Man page
chrID,BinData-method Man page
.computeStat Man page
constructBins Man page
conv_1S Man page
conv_2S Man page
coord Man page
coord,BinData-method Man page
empFDR Man page
empFDR,MosaicsPeak-method Man page
.emZ1_2S Man page
.eStepZ1_2S Man page
estimates Man page
estimates,MosaicsFit-method Man page
estimates,MosaicsHMM-method Man page
export Man page
.exportBED Man page
.exportGFF Man page
export,MosaicsPeak-method Man page
export,MosaicsPeak-method Man page
.exportTXT Man page
extractReads Man page
extractReads,MosaicsPeak-method Man page
filterPeak Man page
filterPeak,MosaicsPeak-method Man page
findSummit Man page
findSummit,MosaicsPeak-method Man page
gcContent Man page
gcContent,BinData-method Man page
generateWig Man page
.getParamZ0 Man page
.getPH_1S Man page
.getPH_2S Man page
.getPi0 Man page
input Man page
input,BinData-method Man page
mappability Man page
mappability,BinData-method Man page
.margDist_1S Man page
.margDist_2S Man page
.margDistZ1_1S Man page
.margDistZ1_2S Man page
mosaics Man page
mosaicsFit Man page
mosaicsFit,BinData-method Man page
mosaicsFit,BinData-method Man page
MosaicsFit-class Man page
MosaicsFitEst-class Man page
mosaicsFitHMM Man page
mosaicsFitHMM,MosaicsFit-method Man page
.mosaicsFit_IO Man page
.mosaicsFit_OS Man page
MosaicsFitParam-class Man page
.mosaicsFit_TS Man page
MosaicsHMM-class Man page
mosaics-package Man page
mosaicsPeak Man page
MosaicsPeak-class Man page
mosaicsPeakHMM Man page
mosaicsPeakHMM,MosaicsHMM-method Man page
mosaicsPeak,MosaicsFit-method Man page
MosaicsPeakParam-class Man page
mosaicsRunAll Man page
.mosaicsZ0_IO Man page
.mosaicsZ0_OS Man page
.mosaicsZ0_TS Man page
.mosaicsZ1_1S Man page
.mosaicsZ1_2S Man page
.mStepZ1_2S Man page
.peakCall Man page
plot,BinData,missing-method Man page
.plotGOF Man page
plot,MosaicsFit,ANY-method Man page
plot,MosaicsHMM,missing-method Man page
plot,MosaicsPeak,missing-method Man page
postProb Man page
postProb,MosaicsPeak-method Man page
print,BinData-method Man page
print,MosaicsFit-method Man page
print,MosaicsHMM-method Man page
print,MosaicsPeak-method Man page
.processBin_MGC Man page
.processBin_MGCX Man page
.processBin_X Man page
read Man page
readBins Man page
readCoverage Man page
readCoverage,MosaicsPeak-method Man page
read,MosaicsPeak-method Man page
.reportSummary Man page
.rlmFit_IO Man page
.rlmFit_OS Man page
.rlmFit_TS Man page
seqDepth Man page
seqDepth,BinData-method Man page
seqDepth,MosaicsFit-method Man page
seqDepth,MosaicsHMM-method Man page
seqDepth,MosaicsPeak-method Man page
show,BinData-method Man page
show,MosaicsFit-method Man page
show,MosaicsHMM-method Man page
show,MosaicsPeak-method Man page
tagCount Man page
tagCount,BinData-method Man page
TagData-class Man page
.validDataType Man page
.validLocation Man page
.validType Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/adjustBoundary.R R/base_adapGridMosaicsZ0_IO.R R/base_adapGridMosaicsZ0_OS.R R/base_adapGridMosaicsZ0_TS.R R/base_annotateHMM.R R/base_annotatePeak.R R/base_calcModelBIC.R R/base_calcPN.R R/base_calcYbdAll.R R/base_computeStat.R R/base_constructExtRead.R R/base_convolution_1S_cpp.R R/base_convolution_2S_cpp.R R/base_cpp_call.R R/base_export.R R/base_extractPostProb.R R/base_fitHMM.R R/base_getParamZ0.R R/base_getPi0.R R/base_loadReadData.R R/base_logLik.R R/base_margDist_1S.R R/base_margDist_2S.R R/base_mosaicsZ0.R R/base_mosaicsZ1_1S.R R/base_mosaicsZ1_2S.R R/base_peakCall.R R/base_plotGOF.R R/base_plotGOFHMM.R R/base_reportSummary.R R/base_rlmFit_IO.R R/base_rlmFit_OS.R R/base_rlmFit_TS.R R/base_trimExtend.R R/constructBins.R R/extractReads.R R/filterPeak.R R/findSummit.R R/generateWig.R R/methods_BinData.R R/methods_MosaicsFit.R R/methods_MosaicsHMM.R R/methods_MosaicsPeak.R R/mosaicsFit.R R/mosaicsFitHMM.R R/mosaicsPeak.R R/mosaicsPeakHMM.R R/mosaicsRunAll.R R/readBins.R
build
build/vignette.rds
inst
inst/Perl
inst/Perl/convert_csem_format.pl
inst/Perl/csem_wrapper.pl
inst/Perl/extract_coord_PET.pl
inst/Perl/extract_coord_SET.pl
inst/Perl/process_readfiles_PET.pl
inst/Perl/process_readfiles_SET.pl
inst/Perl/readfile2wig_PET.pl
inst/Perl/readfile2wig_SET.pl
inst/doc
inst/doc/mosaics-example.R
inst/doc/mosaics-example.Rnw
inst/doc/mosaics-example.pdf
man
man/BinData-class.Rd man/MosaicsFit-class.Rd man/MosaicsFitEst-class.Rd man/MosaicsFitParam-class.Rd man/MosaicsHMM-class.Rd man/MosaicsPeak-class.Rd man/MosaicsPeakParam-class.Rd man/TagData-class.Rd man/adjustBoundary.Rd man/constructBins.Rd man/estimates.Rd man/export.Rd man/extractReads.Rd man/findSummit.Rd man/fllterPeak.Rd man/generateWig.Rd man/mosaics-internal.Rd man/mosaics-package.Rd man/mosaicsFit.Rd man/mosaicsFitHMM.Rd man/mosaicsPeak.Rd man/mosaicsPeakHMM.Rd man/mosaicsRunAll.Rd man/readBins.Rd
src
src/convolution_1S.cpp
src/convolution_2S.cpp
src/emHMM.cpp
src/stack.cpp
src/updatePiMat.cpp
src/viterbi.cpp
vignettes
vignettes/Figure4a.pdf
vignettes/Figure4b.pdf
vignettes/Figure5a.pdf
vignettes/Figure5b.pdf
vignettes/Figure5c.pdf
vignettes/Figure5d.pdf
vignettes/GOF_matchLow.pdf
vignettes/GOF_rMOM.pdf
vignettes/igv.pdf
vignettes/mosaics-example.Rnw
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