Files in Haplin

Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

NEWS.md 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/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.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/getDyads.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/f.create.missingness.matrix.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/getTriads.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 inst/doc/A_Haplin_intro_installation.Rmd inst/doc/E_hapRelEff.R inst/doc/D_Running_Haplin_on_cluster.Rmd inst/doc/C_Running_Haplin.R 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/B_Reading_data.Rmd tests/testthat.R tests/testthat/test_7_haplinStrat.R tests/testthat/common_vars.R tests/testthat/test-getDyads.R tests/testthat/test_2_loading.R tests/testthat/test_8_helpFunctions-getFamilies.R tests/testthat/test_1_reading.R tests/testthat/test_6_haplinSlide.R tests/testthat/test_3_getPart.R tests/testthat/test-getFullTriads.R tests/testthat/test_8_helpFunctions-getChildren.R tests/testthat/test_8_helpFunctions-showPheno.R tests/testthat/test_8_helpFunctions-showGen.R tests/testthat/test_5_haplin.R tests/testthat/test_4_preprocess.R tests/testthat/test_8_helpFunctions-showSNPnames.R tests/testthat/test_9_plotting.R vignettes/A_Haplin_intro_installation.Rmd vignettes/D_Running_Haplin_on_cluster.Rmd vignettes/E_hapRelEff.Rmd vignettes/C_Running_Haplin.Rmd vignettes/B_Reading_data.Rmd 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/f.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