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

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.

Author
Hakon K. Gjessing
Date of publication
2016-05-26 17:44:32
Maintainer
Hakon K. Gjessing <hakon.gjessing@fhi.no>
License
GPL (>= 2)
Version
6.0.1
URLs

View on CRAN

Man pages

cbindFiles
Combine a sequence of files by columns
convertPed
Convert large ped files by creating unique IDs, converting...
gwaaToHaplin
Convert a loaded GenABEL 'gwaa.data' object to a Haplin...
gxe
Test for gene-environment interaction
haplin
Fitting log-linear models to case-parent triad and/or...
haplinSlide
Fit 'haplin' in a series of sliding windows over a sequence...
haplinStrat
Fit 'haplin' to each subset/stratum of data, determined by...
haplinTDT
Transmission disequilibrium tests for case-parent triad data
hapPower
Power simulation for association analyses with Haplin
hapRun
Simulates genetic data and runs Haplin for each simulation
hapSim
Simulation of genetic data in Haplin format
haptable
Create haplin table
lineByLine
Line-by-line modification of files
output
Save files with summary, table, and plot from a haplin...
pedToHaplin
Convert from ped format data to Haplin format
plot.haplin
Plot a haplin object
plot.haplinTDT
Plot a haplinTDT object
plot.haptable
Plot a haptable object
pQQ
QQ-plot with confidence intervals for a vector of p-values
prepPed
Extract family and phenotype information from a ped-format...
print.haplin
Print a haplin object
print.summary.haplin
Print the summary of a haplin object
rbindFiles
Combine a sequence of files by rows
snpPos
Find the column numbers of SNP identifiers/SNP numbers in a...
snpPower
Power calculations for a single SNP
snpSampleSize
Sample size calculations for a single SNP
suest
Compute a joint p-value for a list of haplin fits (usually...
summary.haplin
Summary of a haplin object
summary.haplinTDT
Summary of a haplinTDT object
toDataFrame
Stack dataframes from haplinSlide into a single dataframe

Files in this package

Haplin
Haplin/inst
Haplin/inst/doc
Haplin/inst/doc/index.html
Haplin/inst/doc/Haplin_data_format.pdf
Haplin/inst/doc/Haplin_power.pdf
Haplin/NAMESPACE
Haplin/R
Haplin/R/haplin.R
Haplin/R/suest.R
Haplin/R/print.suest.R
Haplin/R/f.sort.alleles.R
Haplin/R/f.repl.thin.R
Haplin/R/f.var.covar.R
Haplin/R/f.prep.reference.R
Haplin/R/f.EM.missing.R
Haplin/R/f.sort.alleles.cc.R
Haplin/R/uniqueID.R
Haplin/R/textlabel.R
Haplin/R/f.fill.effects.R
Haplin/R/f.prep.dataout.R
Haplin/R/hapPower.R
Haplin/R/snpSampleSize.R
Haplin/R/print.gxe.R
Haplin/R/f.final.loglike.R
Haplin/R/summary.tri.glm.R
Haplin/R/f.posttest.R
Haplin/R/toDataFrame.R
Haplin/R/output.R
Haplin/R/f.vis.R
Haplin/R/f.split.vector.R
Haplin/R/summary.haplin.R
Haplin/R/summary.haplinStrat.R
Haplin/R/f.redistribute.R
Haplin/R/f.design.make.R
Haplin/R/f.prep.data.R
Haplin/R/haptable.haplinStrat.R
Haplin/R/coef.haplin.R
Haplin/R/plot.haplin.R
Haplin/R/f.make.index.R
Haplin/R/haptable.R
Haplin/R/print.tri.glm.R
Haplin/R/f.args.from.info.R
Haplin/R/print.haplin.R
Haplin/R/f.check.pars.R
Haplin/R/f.sep.data.R
Haplin/R/f.post.poo.diff.R
Haplin/R/f.preliminary.freq.R
Haplin/R/pedToHaplin.R
Haplin/R/f.Rplot.R
Haplin/R/print.summary.haplin.R
Haplin/R/f.create.tag.R
Haplin/R/dframe.R
Haplin/R/haptable.gxe.R
Haplin/R/f.HWE.design.R
Haplin/R/haplinStrat.R
Haplin/R/f.jackknife.R
Haplin/R/f.pos.in.grid.R
Haplin/R/convertPed.R
Haplin/R/f.coefnames.R
Haplin/R/f.ped.to.mfc.R
Haplin/R/f.groupsum.R
Haplin/R/f.tri.glm.R
Haplin/R/f.prob.R
Haplin/R/print.info.R
Haplin/R/f.debug.pvalues.R
Haplin/R/as.dframe.R
Haplin/R/f.split.matrix.R
Haplin/R/f.sim.R
Haplin/R/f.suest.R
Haplin/R/f.post.diff.R
Haplin/R/pQQ.R
Haplin/R/f.matrix.to.list.R
Haplin/R/plot.haptable.R
Haplin/R/f.data.R
Haplin/R/lineConvert.R
Haplin/R/f.data.ready.R
Haplin/R/postTest.R
Haplin/R/dumpTab.R
Haplin/R/coef.haptable.R
Haplin/R/rbindFiles.R
Haplin/R/hapRun.R
Haplin/R/f.hapTests.R
Haplin/R/f.printlist.R
Haplin/R/gwaaToHaplin.R
Haplin/R/readData.R
Haplin/R/f.catch.R
Haplin/R/f.posttest.score.R
Haplin/R/print.summary.tri.glm.R
Haplin/R/haplinSlide.R
Haplin/R/print.haplinSlide.R
Haplin/R/f.like.ratio.R
Haplin/R/print.haplinStrat.R
Haplin/R/tdt.R
Haplin/R/gxe.R
Haplin/R/f.pos.match.R
Haplin/R/f.post.contrasts.R
Haplin/R/f.bdiag.R
Haplin/R/f.scoretest.R
Haplin/R/coef.tri.glm.R
Haplin/R/hapSim.R
Haplin/R/snpPos.R
Haplin/R/f.hapArg.R
Haplin/R/print.HWE.test.R
Haplin/R/f.hapSim.R
Haplin/R/snpPower.R
Haplin/R/haptable.haplinSlide.R
Haplin/R/lineByLine.R
Haplin/R/f.rand.geno.R
Haplin/R/f.read.data.R
Haplin/R/f.plot.effects.R
Haplin/R/f.sel.haplos.R
Haplin/R/haptable.default.R
Haplin/R/f.pos.to.haplocomb.R
Haplin/R/f.get.data.R
Haplin/R/f.QQconf.R
Haplin/R/haptable.haplin.R
Haplin/R/f.haptable.list.R
Haplin/R/f.sel.markers.R
Haplin/R/f.get.marker.names.R
Haplin/R/f.HWE.R
Haplin/R/f.aggregate.R
Haplin/R/cbindFiles.R
Haplin/R/prepPed.R
Haplin/R/f.compute.effects.R
Haplin/R/f.post.chisq.R
Haplin/R/f.windows.R
Haplin/MD5
Haplin/DESCRIPTION
Haplin/man
Haplin/man/pQQ.Rd
Haplin/man/suest.Rd
Haplin/man/hapRun.Rd
Haplin/man/haptable.Rd
Haplin/man/hapSim.Rd
Haplin/man/snpPower.Rd
Haplin/man/convertPed.Rd
Haplin/man/prepPed.Rd
Haplin/man/pedToHaplin.Rd
Haplin/man/toDataFrame.Rd
Haplin/man/gwaaToHaplin.Rd
Haplin/man/snpSampleSize.Rd
Haplin/man/lineByLine.Rd
Haplin/man/plot.haplinTDT.Rd
Haplin/man/rbindFiles.Rd
Haplin/man/snpPos.Rd
Haplin/man/haplinTDT.Rd
Haplin/man/print.haplin.Rd
Haplin/man/output.Rd
Haplin/man/summary.haplinTDT.Rd
Haplin/man/haplin.Rd
Haplin/man/plot.haplin.Rd
Haplin/man/summary.haplin.Rd
Haplin/man/haplinStrat.Rd
Haplin/man/print.summary.haplin.Rd
Haplin/man/cbindFiles.Rd
Haplin/man/hapPower.Rd
Haplin/man/plot.haptable.Rd
Haplin/man/haplinSlide.Rd
Haplin/man/gxe.Rd