API for Bioconductor-mirror/BiSeq
Processing and analyzing bisulfite sequencing data

Global functions
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 Source code
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 Source code
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 Source code
binomLikelihoodSmooth,ANY-method Man page
categorialColors Source code
clusterSites Man page Source code
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 Source code
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 Source code
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 Source code
covBoxplots,BSraw-method Man page
covStatistics Man page
covStatistics,BSraw-method Man page
covStatistics,BSrel-method Man page
covStatistics.raw Source code
covStatistics.rel Source code
estLocCor Man page Source code
estLocCor,list-method Man page
filterByCov Man page Source code
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
filterBySharedRegions_BSraw Source code
filterBySharedRegions_BSrel Source code
findDMRs Man page Source code
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 Source code
globalTest,ANY,BSrel-method Man page
limitCov Man page Source code
limitCov,BSraw,numeric-method Man page
logisticRegression Man page Source code
logisticRegression,formula,character,BSrel,missing-method Man page
logisticRegression,formula,character,BSrel,numeric-method Man page
makeVariogram Man page Source code
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 Source code
plotBindingSites,BSraw,GRanges-method Man page
plotBindingSites,BSrel,GRanges-method Man page
plotMeth Man page Source code
plotMeth,BSraw,BSrel,GRanges-method Man page
plotMethMap Man page Source code
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 Source code
plotSmoothMeth,BSrel,GRanges,ANY,logical-method Man page
plotSmoothMeth,BSrel,GRanges,ANY,missing-method Man page
predictMeth Man page Source code
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 Source code
rawToRel,BSraw-method Man page
readBismark Man page Source code
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 Source code
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
summarizeRegions_BSraw Source code
summarizeRegions_BSrel Source code
testClusters Man page Source code
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
triangularWeight Source code
trimClusters Man page Source code
trimClusters,list,missing-method Man page
trimClusters,list,numeric-method Man page
vario Man page
variogram Source code
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
writeBED_BSraw Source code
writeBED_BSrel Source code
Bioconductor-mirror/BiSeq documentation built on July 1, 2017, 4:08 a.m.