Files in Haplin
Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
MD5
NAMESPACE
DESCRIPTION
R/pedToHaplin.R
R/f.Rplot.R
R/genDataLoad.R
R/haptable.default.R
R/f.prep.dataout.R
R/f.sort.alleles.cc.R
R/f.prob.R
R/summary.haplin.R
R/f.sort.alleles.R
R/f.coefnames.R
R/f.tri.glm.R
R/getDyads_or_Triads.R
R/dframe.R
R/f.plot.effects.R
R/f.sim.R
R/coef.haptable.R
R/f.debug.pvalues.R
R/haplinStrat.R
R/f.get.which.gen.el.R
R/plot.haptable.R
R/genDataPreprocess.R
R/plot.haplinStrat.R
R/print.summary.tri.glm.R
R/f.hapSim.R
R/initParallelRun.R
R/f.ped.to.mfc.new.R
R/snpPower.R
R/f.b.asymp.R
R/print.haplin.R
R/hapSim.R
R/f.check.pars0.R
R/f.catch0.R
R/f.get.data.R
R/output.R
R/rbindFiles.R
R/haplinSlide.R
R/f.freq.table.R
R/f.hapArg.R
R/JohnsonFit.R
R/f.data.ready.R
R/summary.haplinStrat.R
R/f.suest.R
R/genDataGetPart.R
R/hapPowerAsymp.R
R/convertPed.R
R/f.EM.missing.R
R/hapRun.R
R/f.pos.match.R
R/pQQ.R
R/f.posttest.score.R
R/f.a.asymp.R
R/f.args.from.info0.R
R/f.vis.R
R/f.post.diff.R
R/f.args.from.info.R
R/postTest.R
R/f.HWE.design.R
R/f.data.R
R/f.prep.data.R
R/coef.haptable.hapSlide.R
R/f.get.gen.data.cols.R
R/f.get.marker.names.R
R/f.scoretest.R
R/f.fill.effects.R
R/f.compute.effects.R
R/genDataRead.R
R/f.catch.R
R/plot.haplinSlide.R
R/f.bdiag.R
R/f.gwaa.to.ff.R
R/hapCovar.R
R/summary.tri.glm.R
R/f.post.chisq.R
R/f.prep.reference.R
R/lineConvert.R
R/nsnps.R
R/f.groupsum.R
R/f.sort.alleles0.R
R/getMothers.R
R/f.mat.asymp.R
R/f.expand.alleles.R
R/f.check.unique.ids.R
R/textlabel.R
R/haptable.R
R/f.matrix.to.list.R
R/f.post.poo.diff.R
R/f.insert.row.R
R/f.windows.R
R/f.design.get.R
R/getFathers.R
R/print.info.R
R/f.HWE.R
R/getChildren.R
R/f.split.matrix.R
R/snpSampleSize.R
R/f.post.contrasts.R
R/f.var.covar.asymp.R
R/f.posttest.R
R/haptable.gxe.R
R/f.repl.thin.R
R/f.preliminary.freq0.R
R/f.create.snp.names.R
R/haptable.haplinSlide.R
R/haptable.haplin.R
R/plotPValues.R
R/f.repl.thin0.R
R/showPheno.R
R/f.sep.data.R
R/f.like.ratio.R
R/f.HWE.design0.R
R/f.make.index.R
R/haptable.haplinStrat.R
R/f.sel.markers.R
R/print.haplin.data.R
R/f.redistribute.R
R/f.sel.haplos.R
R/gxe.R
R/f.create.tag.R
R/dumpTab.R
R/f.final.loglike.R
R/f.get.which.gen.el.names.R
R/f.beta.haplo.freq.asymp.R
R/coef.haplin.R
R/print.HWE.test.R
R/f.check.pars.R
R/f.aggregate.R
R/f.prob.asymp.R
R/f.sort.alleles.cc0.R
R/print.summary.haplin.R
R/f.rand.geno.R
R/haplin0.R
R/nfam.R
R/f.HWE0.R
R/haplinSlide0.R
R/f.read.data.R
R/cbindFiles.R
R/haplinStrat0.R
R/f.match.R
R/nindiv.R
R/f.pos.in.grid.R
R/zzz.R
R/f.ped.to.mfc0.R
R/toDataFrame.R
R/print.haplinStrat.R
R/f.pos.to.haplocomb.R
R/suest.R
R/f.grid.asymp.R
R/f.design.make.R
R/f.haptable.list.R
R/f.make.ff.data.out.R
R/as.dframe.R
R/lineByLine.R
R/plot.haplin.R
R/print.suest.R
R/coef.tri.glm.R
R/f.var.covar.R
R/hapPower.R
R/f.prep.data.parallel.R
R/f.split.vector.R
R/showSNPnames.R
R/f.hapTests.R
R/f.jackknife.R
R/f.sep.data0.R
R/haplin.R
R/showGen.R
R/f.QQconf.R
R/print.haplin.ready.R
R/f.prep.pedIndex.R
R/f.preliminary.freq.R
R/f.extract.freq.R
R/f.data0.R
R/f.printlist.R
R/f.convert.matrix.ff.R
R/snpPos.R
R/hapRelEff.R
R/f.make.out.filename.R
R/print.haplinSlide.R
R/f.extract.ff.numeric.R
R/print.tri.glm.R
R/print.gxe.R
R/finishParallelRun.R
src/Haplin_init.c
src/dists.cc
src/dists.h
inst/CITATION
inst/doc/A_Haplin_intro_installation.Rmd
inst/doc/E_hapRelEff.html
inst/doc/E_hapRelEff.R
inst/doc/D_Running_Haplin_on_cluster.Rmd
inst/doc/C_Running_Haplin.R
inst/doc/B_Reading_data.html
inst/doc/A_Haplin_intro_installation.R
inst/doc/E_hapRelEff.Rmd
inst/doc/D_Running_Haplin_on_cluster.R
inst/doc/B_Reading_data.R
inst/doc/C_Running_Haplin.Rmd
inst/doc/C_Running_Haplin.html
inst/doc/A_Haplin_intro_installation.html
inst/doc/B_Reading_data.Rmd
inst/doc/D_Running_Haplin_on_cluster.html
inst/extdata/qc_all.map
inst/extdata/qc_all_ok_gen.RData
inst/extdata/HAPLIN.trialdata.txt
inst/extdata/add_cov_data2.dat
inst/extdata/qc_all_ok_gen.ffData
inst/extdata/add_cov_data.dat
inst/extdata/exmpl_data.map
inst/extdata/data.dat
inst/extdata/submit_haplin_cluster_rmpi.sh
inst/extdata/HAPLIN.trialdata2.txt
inst/extdata/exmpl_data.ped
build/vignette.rds
vignettes/A_Haplin_intro_installation.Rmd
vignettes/Styrke_artikkel_rmd.bib
vignettes/HAPLIN.trialdata.txt
vignettes/D_Running_Haplin_on_cluster.Rmd
vignettes/E_hapRelEff.Rmd
vignettes/C_Running_Haplin.Rmd
vignettes/HAPLIN.trialdata2.txt
vignettes/B_Reading_data.Rmd
vignettes/graphics/haplin_function_calls.png
vignettes/graphics/haplin_info_struct.png
vignettes/graphics/haplin_result_struct.png
man/genDataLoad.Rd
man/showGen.Rd
man/lineByLine.Rd
man/haptable.Rd
man/plot.haplin.Rd
man/getFathers.Rd
man/pedToHaplin.Rd
man/plot.haptable.Rd
man/cbindFiles.Rd
man/hapSim.Rd
man/getChildren.Rd
man/plotPValues.Rd
man/snpPower.Rd
man/hapRelEff.Rd
man/gxe.Rd
man/nindiv.Rd
man/hapRun.Rd
man/output.Rd
man/create.missingness.matrix.Rd
man/genDataGetPart.Rd
man/f.convert.matrix.ff.Rd
man/f.create.snp.names.Rd
man/rbindFiles.Rd
man/hapPowerAsymp.Rd
man/genDataRead.Rd
man/summary.haplin.Rd
man/hapPower.Rd
man/f.check.unique.ids.Rd
man/f.get.gen.data.cols.Rd
man/snpPos.Rd
man/finishParallelRun.Rd
man/haplinSlide.Rd
man/showPheno.Rd
man/initParallelRun.Rd
man/showSNPnames.Rd
man/nsnps.Rd
man/haplinStrat.Rd
man/getDyads.Rd
man/pQQ.Rd
man/suest.Rd
man/print.summary.haplin.Rd
man/pJohnson.Rd
man/nfam.Rd
man/convertPed.Rd
man/getFullTriads.Rd
man/snpSampleSize.Rd
man/plot.haplinStrat.Rd
man/print.haplin.Rd
man/plot.haplinSlide.Rd
man/getMothers.Rd
man/genDataPreprocess.Rd
man/f.extract.ff.numeric.Rd
man/toDataFrame.Rd
man/haplin.Rd
