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.

Install the latest version of this package by entering the following in R:
install.packages("Haplin")
AuthorHakon K. Gjessing
Date of publication2017-02-28 14:47:43
MaintainerHakon K. Gjessing <hakon.gjessing@fhi.no>
LicenseGPL (>= 2)
Version6.2.0
http://folk.uib.no/gjessing/genetics/software/haplin/

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

hapPowerAsymp: Asymptotic power calculations for genetic association...

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

Functions

cbindFiles Man page
convertPed Man page
gwaaToHaplin Man page
gxe Man page
haplin Man page
haplinSlide Man page
haplinStrat Man page
haplinTDT Man page
hapPower Man page
hapPowerAsymp Man page
hapRun Man page
hapSim Man page
haptable Man page
lineByLine Man page
output Man page
pedToHaplin Man page
plot Man page
plot.haplin Man page
plot.haplinTDT Man page
plot.haptable Man page
pQQ Man page
prepPed Man page
print.haplin Man page
print.summary.haplin Man page
rbindFiles Man page
snpPos Man page
snpPower Man page
snpSampleSize Man page
suest Man page
summary.haplin Man page
summary.haplinTDT Man page
toDataFrame Man page

Files

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

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