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Haplin  

Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
View on CRAN: Click here


Download and install Haplin package within the R console
Install from CRAN:
install.packages("Haplin")

Install from Github:
library("remotes")
install_github("cran/Haplin")

Install by package version:
library("remotes")
install_version("Haplin", "7.3.1")



Attach the package and use:
library("Haplin")
Maintained by
Hakon K. Gjessing
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2009-05-27
Latest Update: 2022-05-20
Description:
Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".
How to cite:
Hakon K. Gjessing (2009). Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes. R package version 7.3.1, https://cran.r-project.org/web/packages/Haplin
Previous versions and publish date:
3.0.1 (2009-05-27 10:59), 3.0.2 (2010-01-10 09:04), 3.5 (2010-05-26 10:46), 4.0 (2012-01-27 12:17), 4.1 (2012-03-16 11:04), 5.0.1 (2013-03-08 17:44), 5.0.2 (2013-03-18 15:49), 5.0 (2013-02-06 14:41), 5.2 (2013-05-02 15:20), 5.3 (2013-05-23 11:10), 5.5 (2015-05-15 21:42), 6.0.1 (2016-05-26 17:44), 6.0 (2016-05-25 11:17), 6.2.0 (2017-02-28 14:47), 6.2.1 (2017-10-18 23:32), 7.0.0 (2018-05-28 00:50), 7.1.0 (2019-04-17 23:30), 7.2.2 (2020-01-07 15:40), 7.2.3 (2020-09-07 08:50), 7.3.0 (2022-05-20 14:00)
Other packages that cited Haplin R package
View Haplin citation profile
Other R packages that Haplin depends, imports, suggests or enhances
Functions, R codes and Examples using the Haplin R package
Some associated functions: cbindFiles . convertPed . create.missingness.matrix . f.check.unique.ids . f.convert.matrix.ff . f.create.snp.names . f.extract.ff.numeric . f.get.gen.data.cols . finishParallelRun . genDataGetPart . genDataLoad . genDataPreprocess . genDataRead . getChildren . getDyads . getFathers . getFullTriads . getMothers . gxe . hapPower . hapPowerAsymp . hapRelEff . hapRun . hapSim . haplin . haplinSlide . haplinStrat . haptable . initParallelRun . lineByLine . nfam . nindiv . nsnps . output . pJohnson . pQQ . pedToHaplin . plot.haplin . plot.haplinSlide . plot.haplinStrat . plot.haptable . plotPValues . print.haplin . print.summary.haplin . rbindFiles . showGen . showPheno . showSNPnames . snpPos . snpPower . snpSampleSize . suest . summary.haplin . toDataFrame . 
Some associated R codes: JohnsonFit.R . as.dframe.R . cbindFiles.R . coef.haplin.R . coef.haptable.R . coef.haptable.hapSlide.R . coef.tri.glm.R . convertPed.R . dframe.R . dumpTab.R . f.EM.missing.R . f.HWE.R . f.HWE.design.R . f.HWE.design0.R . f.HWE0.R . f.QQconf.R . f.Rplot.R . f.a.asymp.R . f.aggregate.R . f.args.from.info.R . f.args.from.info0.R . f.b.asymp.R . f.bdiag.R . f.beta.haplo.freq.asymp.R . f.catch.R . f.catch0.R . f.check.pars.R . f.check.pars0.R . f.check.unique.ids.R . f.coefnames.R . f.compute.effects.R . f.convert.matrix.ff.R . f.create.snp.names.R . f.create.tag.R . f.data.R . f.data.ready.R . f.data0.R . f.debug.pvalues.R . f.design.get.R . f.design.make.R . f.expand.alleles.R . f.extract.ff.numeric.R . f.extract.freq.R . f.fill.effects.R . f.final.loglike.R . f.freq.table.R . f.get.data.R . f.get.gen.data.cols.R . f.get.marker.names.R . f.get.which.gen.el.R . f.get.which.gen.el.names.R . f.grid.asymp.R . f.groupsum.R . f.gwaa.to.ff.R . f.hapArg.R . f.hapSim.R . f.hapTests.R . f.haptable.list.R . f.insert.row.R . f.jackknife.R . f.like.ratio.R . f.make.ff.data.out.R . f.make.index.R . f.make.out.filename.R . f.mat.asymp.R . f.match.R . f.matrix.to.list.R . f.ped.to.mfc.new.R . f.ped.to.mfc0.R . f.plot.effects.R . f.pos.in.grid.R . f.pos.match.R . f.pos.to.haplocomb.R . f.post.chisq.R . f.post.contrasts.R . f.post.diff.R . f.post.poo.diff.R . f.posttest.R . f.posttest.score.R . f.preliminary.freq.R . f.preliminary.freq0.R . f.prep.data.R . f.prep.data.parallel.R . f.prep.dataout.R . f.prep.pedIndex.R . f.prep.reference.R . f.printlist.R . f.prob.R . f.prob.asymp.R . f.rand.geno.R . f.read.data.R . f.redistribute.R . f.repl.thin.R . f.repl.thin0.R . f.scoretest.R . f.sel.haplos.R . f.sel.markers.R . f.sep.data.R . f.sep.data0.R . f.sim.R . f.sort.alleles.R . f.sort.alleles.cc.R . f.sort.alleles.cc0.R . f.sort.alleles0.R . f.split.matrix.R . f.split.vector.R . f.suest.R . f.tri.glm.R . f.var.covar.R . f.var.covar.asymp.R . f.vis.R . f.windows.R . finishParallelRun.R . genDataGetPart.R . genDataLoad.R . genDataPreprocess.R . genDataRead.R . getChildren.R . getDyads_or_Triads.R . getFathers.R . getMothers.R . gxe.R . hapCovar.R . hapPower.R . hapPowerAsymp.R . hapRelEff.R . hapRun.R . hapSim.R . haplin.R . haplin0.R . haplinSlide.R . haplinSlide0.R . haplinStrat.R . haplinStrat0.R . haptable.R . haptable.default.R . haptable.gxe.R . haptable.haplin.R . haptable.haplinSlide.R . haptable.haplinStrat.R . initParallelRun.R . lineByLine.R . lineConvert.R . nfam.R . nindiv.R . nsnps.R . output.R . pQQ.R . pedToHaplin.R . plot.haplin.R . plot.haplinSlide.R . plot.haplinStrat.R . plot.haptable.R . plotPValues.R . postTest.R . print.HWE.test.R . print.gxe.R . print.haplin.R . print.haplin.data.R . print.haplin.ready.R . print.haplinSlide.R . print.haplinStrat.R . print.info.R . print.suest.R . print.summary.haplin.R . print.summary.tri.glm.R . print.tri.glm.R . rbindFiles.R . showGen.R . showPheno.R . showSNPnames.R . snpPos.R . snpPower.R . snpSampleSize.R . suest.R . summary.haplin.R . summary.haplinStrat.R . summary.tri.glm.R . textlabel.R . toDataFrame.R . zzz.R .  Full Haplin package functions and examples
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