first commit
second commit
removed some files
Revert "first commit"

This reverts commit 4c6770776ad3dd51be803390ec3f13369e93ef36.

Conflicts:
	DESCRIPTION
	NAMESPACE
	R/BF.cutoff.R
	R/BF.ecdf.R
	R/Fb.f.R
	R/Pr.S.R
	R/Pr.S.cp.R
	R/Pr.S.up.R
	R/Pr.f.R
	R/Q2.R
	R/Q3.R
	R/QL.R
	R/R.merger.R
	R/Rcpp.merger.R
	R/add.counts.R
	R/add.counts.chr.R
	R/add.siteUID.R
	R/any.overlap.sites.R
	R/any.overlap.sites.allchr.R
	R/any.overlaps.R
	R/append.effectsign.R
	R/assign.groups.R
	R/attach.TsiteOLP.R
	R/attach.pmeans.cutoff.R
	R/attach.pmeans.score.R
	R/attach.winScoreP.R
	R/attachP.BF.cutoff.R
	R/b.f.R
	R/batch.jobs.R
	R/bf.filter.R
	R/bf.filter.selSites.R
	R/bg.N.R
	R/calculate.gmeans.R
	R/choose.events.cutoff.R
	R/choose.site.pattern.R
	R/choose.sitePattern.R
	R/choose.sitePattern.byChr.R
	R/clean.dupcontr.sigsites.R
	R/clean.dupcontr.sites.R
	R/clean.nonuniqPatt.R
	R/clean.sitePatt.R
	R/cleanup.on.gmeans.R
	R/code.contrast.R
	R/code.pattern.R
	R/comb.hyperHypo.R
	R/combine.2rl.R
	R/combine.report.R
	R/common.expandIdx.R
	R/compete.patt.R
	R/compute.T.R
	R/compute.Tbar.R
	R/compute.beta.para.2.R
	R/compute.beta.para.3.R
	R/compute.beta.para.R
	R/compute.cutoff.R
	R/compute.minB.p.R
	R/compute.minB.para.R
	R/compute.p.R
	R/compute.pmeans.R
	R/compute.qvalues.R
	R/compute.v.R
	R/consolidate.lows.R
	R/construct.contrast.objs.R
	R/construct.contrasts.R
	R/create.ws.dir.R
	R/cut.wins.R
	R/cut.wins2.R
	R/cutoff.sites.R
	R/default.contrastList.R
	R/default.pattContrast.R
	R/denoiseSignal.R
	R/dir.poiComparePerWin.R
	R/disjoin.sites.R
	R/dpt.qvalues.R
	R/dpt.report.postprocess.R
	R/dpt.syshold.R
	R/dptMethods-package.r
	R/dptMethods2-internal.R
	R/dptworkflow.r
	R/e.res.BF.ecdf.R
	R/escore.comp.R
	R/est.NB.R
	R/est.beta.para.R
	R/est.grpMeans.R
	R/event.allPossiblePatterns.R
	R/event.patternsToScan.R
	R/event.prob.R
	R/event.prob.cut.R
	R/event.prob.mx.R
	R/event.v.prob.R
	R/events.cutoff.R
	R/events.score.R
	R/extend.QuESTFimoNames.R
	R/extend.seq.R
	R/extend.tbs.R
	R/extract.info.fromQuESTPeakOutput.R
	R/extract.info.fromQuESTRegioOutput.R
	R/f.f.R
	R/find.cutoff.R
	R/find.cutoff.objective.R
	R/findBest.escoreCutoff.R
	R/flattern.testReport.R
	R/format.data.lme.R
	R/format.sites4diffTest.R
	R/gen.poi.R
	R/get.commandArg.R
	R/get.count.tb.sample.R
	R/get.difftest.flatReport.R
	R/get.e.res.R
	R/get.lambda.R
	R/get.lambdaVar.R
	R/get.mappedCountTab.R
	R/get.n.cpus.R
	R/get.n.reads.sample.R
	R/get.p.R
	R/get.pmeans.cut.R
	R/get.postLambda3.var.R
	R/get.postLogLambda2.R
	R/get.postLogLambda22.R
	R/get.postLogLambda3.R
	R/get.postMean.R
	R/get.postMean.cutoffs.aux.R
	R/get.postMean.cutoffs.aux2.R
	R/get.postmean.var.R
	R/get.questRegions.R
	R/get.reads.R
	R/get.reads.fromJoinedSamples.R
	R/get.reads.poi.R
	R/get.sequence.R
	R/get.sequence.chr.R
	R/get.sharedSource.R
	R/get.sharedSrc.R
	R/get.sig.R
	R/get.sigvar.R
	R/get.siteSig.R
	R/get.str.chr.R
	R/get.str.smpsheet.R
	R/get.w.R
	R/get.w.var.R
	R/get.w3.R
	R/get.w3.var.R
	R/get.w3Chr.R
	R/get.wiSum.R
	R/get.winsize.R
	R/get.winsize.input.R
	R/get.ws.R
	R/get.ws.chrs.R
	R/get.ws.path.R
	R/get.wsoption.para.R
	R/get.wsoption.path.R
	R/h.f.R
	R/h.f_1.R
	R/identify.win.overlap.R
	R/if.overlap.R
	R/if.parallel.R
	R/init-filtering.r
	R/init.ws.dirs.R
	R/join.counts.R
	R/join.counts.chr.R
	R/join.samples.R
	R/join.samples.chr.R
	R/join.sites.R
	R/lambda.R
	R/load.analysisData.R
	R/load.diffTestData.R
	R/load.init.ws.R
	R/load.mappedData.R
	R/load.mappedFile.R
	R/load.mixPoiData.R
	R/load.pattRecogData.R
	R/load.reportData.R
	R/load.ws.image.R
	R/logit.f.R
	R/make.RContrast.R
	R/make.reportContrast.R
	R/map.region.2.R
	R/map.region.R
	R/map.region.chr.2.R
	R/map.regions.R
	R/map.regs.chr.R
	R/match.mx.R
	R/match.patt.pattmx.R
	R/match.pattern.win.R
	R/mean.qint.R
	R/merge.fimo.site.R
	R/merge.samples.R
	R/mixPois_eWin.R
	R/mk.sites.report.R
	R/node.compute.Pr.R
	R/node.get.p.n.R
	R/node.pick.range.R
	R/node.set.Pr.R
	R/node.set.Pr.aux.R
	R/node.set.significance.R
	R/node.set.significance.aux.R
	R/norm.tbs.R
	R/normalize.pmeans.R
	R/normalize.sig.R
	R/normalize.signal.R
	R/overlap.commonSet.R
	R/overlap.proportion.R
	R/overlap.size.R
	R/overlap.wins.test.element.R
	R/overlapProp.byID.R
	R/par.poiComparePerWin.R
	R/para.addCounts.R
	R/para.joinCounts.R
	R/para.joinSamples.R
	R/para.testRatios.R
	R/paraApply.R
	R/paraApply2.R
	R/paraLapply.R
	R/patt.summary.R
	R/pattSummary.2dataframe.R
	R/pattern.design.R
	R/pattern.events.R
	R/plot.multivariate.R
	R/poiComparePerWin.R
	R/process.diffTest.R
	R/process.report.R
	R/range.poi.R
	R/range.pois.R
	R/ranged.e.TF.R
	R/ranged.e.scores.R
	R/rangedSites.R
	R/read.refgenome.R
	R/remove.dupcontr.R
	R/remove.duplicateRegion.R
	R/remove.dupsite.R
	R/replace.names.R
	R/rgam.main2.R
	R/rgam2.R
	R/rmultin.R
	R/save.ws.R
	R/save.ws.image.R
	R/score.ecdf.R
	R/search.sites.R
	R/search.sites.v2.R
	R/sel.sigsites.R
	R/sel.sigsites_1.R
	R/selReads.report.R
	R/select.reads.R
	R/select.sig.sites.2.R
	R/select.sig.sites.R
	R/select.siteWins.R
	R/select.sites.BF.cutoff.R
	R/select.sites.GWadj.R
	R/select.sites.R
	R/select.wins.test.element.R
	R/select.wins.test.report.R
	R/shear.sites.R
	R/siteUID.R
	R/size.site.R
	R/start.para.R
	R/stop.para.R
	R/subset.pmeans.R
	R/tabsps.R
	R/test.effect.R
	R/test.effect.rep.R
	R/test.ratios.R
	R/test.ratios.chr.R
	R/trans2rangedData.R
	R/truncate4wd.R
	R/which.max.by.R
	R/which.min.by.R
	R/which.zeroPattern.R
	R/win.den.R
	R/win.movingCount.R
	R/win.movingSum.R
	R/win.overlap.pair.R
	R/win.search.R
	R/win.select.R
	R/write.sites.seqs.R
	man/dptMethods.Rd
Merge branch 'master' of github.com:Jeanie4git/dptmethods