Other packages > Find by keyword >

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", "7.3.2")



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 7.3.2, https://cran.r-project.org/web/packages/Haplin. Accessed 03 Dec. 2024.
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), 7.3.1 (2024-02-08 23:20)
Other packages that cited Haplin R package
View Haplin citation profile
Other R packages that Haplin depends, imports, suggests or enhances
Complete documentation for Haplin
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
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

donut  
Nearest Neighbour Search with Variables on a Torus
Finds the k nearest neighbours in a dataset of specified points, adding the option to wrap certain ...
Download / Learn more Package Citations See dependency  
CRANsearcher  
RStudio Addin for Searching Packages in CRAN Database Based on Keywords
One of the strengths of R is its vast package ecosystem. Indeed, R packages extend from visualizatio ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
FSInteract  
Fast Searches for Interactions
Performs fast detection of interactions in large-scale data using the method of random intersection ...
Download / Learn more Package Citations See dependency  
telemac  
R Interface to the TELEMAC Model Suite
An R interface to the TELEMAC suite for modelling of free surface flow. This includes methods for m ...
Download / Learn more Package Citations See dependency  
EDOtrans  
Euclidean Distance-Optimized Data Transformation
A data transformation method which takes into account the special property of scale non-invariance w ...
Download / Learn more Package Citations See dependency  

23,310

R Packages

200,798

Dependencies

63,203

Author Associations

23,278

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA