API for BiSeq
Processing and analyzing bisulfite sequencing data

Global functions
.annotateGRanges	Source code
.betaRegression	Source code
.binomLikelihoodSmooth	Source code
.categorialColors	Source code
.clusterSites	Source code
.clusterSitesToGR	Source code
.compareTwoSamples	Source code
.covBoxplots	Source code
.covStatistics.raw	Source code
.covStatistics.rel	Source code
.estLocCor	Source code
.filterByCov	Source code
.filterBySharedRegions_BSraw	Source code
.filterBySharedRegions_BSrel	Source code
.findDMRs	Source code
.globalTest	Source code
.limitCov	Source code
.logisticRegression	Source code
.makeVariogram	Source code
.plotBindingSites	Source code
.plotMeth	Source code
.plotMethMap	Source code
.plotSmoothMeth	Source code
.predictMeth	Source code
.rawToRel	Source code
.readBismark	Source code
.smoothVariogram	Source code
.summarizeRegions_BSraw	Source code
.summarizeRegions_BSrel	Source code
.testClusters	Source code
.triangularWeight	Source code
.trimClusters	Source code
.variogram	Source code
.writeBED_BSraw	Source code
.writeBED_BSrel	Source code
BSraw	Man page
BSraw,matrix,matrix,GRanges-method	Man page
BSraw-class	Man page
BSrel	Man page
BSrel,matrix,GRanges-method	Man page
BSrel-class	Man page
DMRs	Man page
annotateGRanges	Man page
annotateGRanges,GRanges,GRanges,character,character-method	Man page
annotateGRanges,GRanges,GRanges,character,integer-method	Man page
annotateGRanges,GRanges,GRanges,character,missing-method	Man page
betaRegression	Man page
betaRegression,formula,character,BSrel,missing-method	Man page
betaRegression,formula,character,BSrel,numeric-method	Man page
betaResults	Man page
betaResultsNull	Man page
binomLikelihoodSmooth	Man page
binomLikelihoodSmooth,ANY-method	Man page
clusterSites	Man page
clusterSites,BSraw,ANY,numeric,missing,missing,missing-method	Man page
clusterSites,BSraw,ANY,numeric,missing,numeric,missing-method	Man page
clusterSites,BSraw,ANY,numeric,numeric,missing,missing-method	Man page
clusterSites,BSraw,ANY,numeric,numeric,numeric,missing-method	Man page
clusterSites,BSraw,ANY,numeric,numeric,numeric,numeric-method	Man page
clusterSites,BSraw,missing,missing,missing,missing,missing-metho	Man page
clusterSites,BSraw,missing,numeric,numeric,numeric,missing-metho	Man page
clusterSites,BSraw,missing,numeric,numeric,numeric,numeric-metho	Man page
clusterSitesToGR	Man page
clusterSitesToGR,BSraw-method	Man page
clusterSitesToGR,BSrel-method	Man page
combine,BSraw,BSraw-method	Man page
combine,BSrel,BSrel-method	Man page
compareTwoSamples	Man page
compareTwoSamples,BSraw,character,character,numeric,numeric-meth	Man page
compareTwoSamples,BSraw,numeric,numeric,numeric,numeric-method	Man page
compareTwoSamples,BSrel,character,character,numeric,numeric-meth	Man page
compareTwoSamples,BSrel,numeric,numeric,numeric,numeric-method	Man page
covBoxplots	Man page
covBoxplots,BSraw-method	Man page
covStatistics	Man page
covStatistics,BSraw-method	Man page
covStatistics,BSrel-method	Man page
estLocCor	Man page
estLocCor,list-method	Man page
filterByCov	Man page
filterByCov,BSraw,missing,logical-method	Man page
filterByCov,BSraw,missing,missing-method	Man page
filterByCov,BSraw,numeric,logical-method	Man page
filterByCov,BSraw,numeric,missing-method	Man page
filterBySharedRegions	Man page
filterBySharedRegions,BSraw,ANY,missing,numeric,missing-method	Man page
filterBySharedRegions,BSraw,ANY,missing,numeric,numeric-method	Man page
filterBySharedRegions,BSraw,ANY,numeric,missing,missing-method	Man page
filterBySharedRegions,BSraw,ANY,numeric,missing,numeric-method	Man page
filterBySharedRegions,BSraw,missing,missing,missing,missing-meth	Man page
filterBySharedRegions,BSraw,missing,missing,missing,numeric-meth	Man page
filterBySharedRegions,BSraw,missing,missing,numeric,missing-meth	Man page
filterBySharedRegions,BSraw,missing,missing,numeric,numeric-meth	Man page
filterBySharedRegions,BSraw,missing,numeric,missing,missing-meth	Man page
filterBySharedRegions,BSraw,missing,numeric,missing,numeric-meth	Man page
filterBySharedRegions,BSrel,ANY,missing,numeric,ANY-method	Man page
filterBySharedRegions,BSrel,ANY,numeric,missing,ANY-method	Man page
filterBySharedRegions,BSrel,missing,missing,missing,ANY-method	Man page
filterBySharedRegions,BSrel,missing,missing,numeric,ANY-method	Man page
filterBySharedRegions,BSrel,missing,numeric,missing,ANY-method	Man page
findDMRs	Man page
findDMRs,data.frame,missing,numeric,logical-method	Man page
findDMRs,data.frame,missing,numeric,missing-method	Man page
findDMRs,data.frame,numeric,numeric,logical-method	Man page
findDMRs,data.frame,numeric,numeric,missing-method	Man page
globalTest	Man page
globalTest,ANY,BSrel-method	Man page
limitCov	Man page
limitCov,BSraw,numeric-method	Man page
logisticRegression	Man page
logisticRegression,formula,character,BSrel,missing-method	Man page
logisticRegression,formula,character,BSrel,numeric-method	Man page
makeVariogram	Man page
makeVariogram,data.frame,logical,missing,missing-method	Man page
makeVariogram,data.frame,logical,missing,numeric-method	Man page
makeVariogram,data.frame,logical,numeric,missing-method	Man page
makeVariogram,data.frame,logical,numeric,numeric-method	Man page
makeVariogram,data.frame,missing,missing,missing-method	Man page
makeVariogram,data.frame,missing,numeric,numeric-method	Man page
methLevel	Man page
methLevel,BSrel-method	Man page
methLevel<-	Man page
methLevel<-,BSrel,matrix-method	Man page
methReads	Man page
methReads,BSraw-method	Man page
methReads<-	Man page
methReads<-,BSraw,matrix-method	Man page
plotBindingSites	Man page
plotBindingSites,BSraw,GRanges-method	Man page
plotBindingSites,BSrel,GRanges-method	Man page
plotMeth	Man page
plotMeth,BSraw,BSrel,GRanges-method	Man page
plotMethMap	Man page
plotMethMap,BSraw,GRanges,factor,logical-method	Man page
plotMethMap,BSraw,GRanges,factor,missing-method	Man page
plotMethMap,BSraw,GRanges,missing,logical-method	Man page
plotMethMap,BSraw,GRanges,missing,missing-method	Man page
plotMethMap,BSrel,GRanges,factor,logical-method	Man page
plotMethMap,BSrel,GRanges,factor,missing-method	Man page
plotMethMap,BSrel,GRanges,missing,logical-method	Man page
plotMethMap,BSrel,GRanges,missing,missing-method	Man page
plotSmoothMeth	Man page
plotSmoothMeth,BSrel,GRanges,ANY,logical-method	Man page
plotSmoothMeth,BSrel,GRanges,ANY,missing-method	Man page
predictMeth	Man page
predictMeth,BSraw,missing,missing,missing-method	Man page
predictMeth,BSraw,missing,missing,numeric-method	Man page
predictMeth,BSraw,numeric,missing,missing-method	Man page
predictMeth,BSraw,numeric,missing,numeric-method	Man page
predictMeth,BSraw,numeric,numeric,numeric-method	Man page
predictedMeth	Man page
promoters	Man page
rawToRel	Man page
rawToRel,BSraw-method	Man page
readBismark	Man page
readBismark,character,DataFrame-method	Man page
readBismark,character,character-method	Man page
readBismark,character,data.frame-method	Man page
rrbs	Man page
smoothVariogram	Man page
smoothVariogram,list,numeric,missing-method	Man page
smoothVariogram,list,numeric,numeric-method	Man page
smoothVariogram,matrix,numeric,missing-method	Man page
smoothVariogram,matrix,numeric,numeric-method	Man page
summarizeRegions	Man page
summarizeRegions,BSraw,GRanges,logical-method	Man page
summarizeRegions,BSraw,GRanges,missing-method	Man page
summarizeRegions,BSrel,GRanges,logical-method	Man page
summarizeRegions,BSrel,GRanges,missing-method	Man page
testClusters	Man page
testClusters,list,missing-method	Man page
testClusters,list,numeric-method	Man page
totalReads	Man page
totalReads,BSraw-method	Man page
totalReads<-	Man page
totalReads<-,BSraw,matrix-method	Man page
trimClusters	Man page
trimClusters,list,missing-method	Man page
trimClusters,list,numeric-method	Man page
vario	Man page
writeBED	Man page
writeBED,BSraw,character,character-method	Man page
writeBED,BSraw,character,missing-method	Man page
writeBED,BSraw,missing,character-method	Man page
writeBED,BSraw,missing,missing-method	Man page
writeBED,BSrel,character,character-method	Man page
writeBED,BSrel,character,missing-method	Man page
writeBED,BSrel,missing,character-method	Man page
writeBED,BSrel,missing,missing-method	Man page