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
BiSeq documentation built on Nov. 8, 2020, 8:05 p.m.