Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes
Version 6.2.0

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.

Browse man pages Browse package API and functions Browse package files

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

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

DifferenceVector Source code
DifferenceVector.nofreq Source code
Hhrr.test Source code
MakeTriosTable Source code
MakeTriosTable.nofreq Source code
MakeTriosTable0 Source code
MakeTriosTable0.nofreq Source code
ReorderAlleles Source code
SelectSubset Source code
Tdt.test Source code
Tdt.test.2allele Source code
Trimm.test Source code
as.dframe Source code
cbindFiles Man page Source code
coef.haplin Source code
coef.haptable Source code
coef.tri.glm Source code
convertPed Man page Source code
dframe Source code
dumpTab Source code
f.HWE Source code
f.HWE.design Source code
f.QQconf Source code
f.Rplot Source code
f.a.asymp Source code
f.aggregate Source code
f.args.from.info Source code
f.b.asymp Source code
f.bdiag Source code
f.beta.haplo.freq.asymp Source code
f.catch Source code
f.check.pars Source code
f.coefnames Source code
f.create.tag Source code
f.data Source code
f.data.ready Source code
f.debug.pvalues Source code
f.design.get Source code
f.design.make Source code
f.fill.effects Source code
f.final.loglike Source code
f.get.data Source code
f.get.marker.names Source code
f.grid.asymp Source code
f.hapArg Source code
f.hapSim Source code
f.hapTests Source code
f.haptable.list Source code
f.jackknife Source code
f.like.ratio Source code
f.make.index Source code
f.mat.asymp Source code
f.match Source code
f.matrix.to.list Source code
f.ped.to.mfc Source code
f.plot.effects Source code
f.pos.in.grid Source code
f.pos.match Source code
f.pos.to.haplocomb Source code
f.post.chisq Source code
f.post.contrasts Source code
f.post.diff Source code
f.post.poo.diff Source code
f.posttest Source code
f.preliminary.freq.new Source code
f.prep.data Source code
f.prep.dataout Source code
f.prep.reference Source code
f.printlist Source code
f.prob Source code
f.prob.asymp Source code
f.rand.geno Source code
f.read.data Source code
f.redistribute Source code
f.repl.thin Source code
f.scoretest Source code
f.sel.haplos Source code
f.sel.markers Source code
f.sep.data Source code
f.sim Source code
f.sort.alleles.cc Source code
f.sort.alleles.new Source code
f.split.matrix Source code
f.split.vector Source code
f.suest Source code
f.var.covar Source code
f.var.covar.asymp Source code
f.windows Source code
gwaaToHaplin Man page Source code
gxe Man page Source code
hapCovar Source code
hapPower Man page Source code
hapPowerAsymp Man page Source code
hapRun Man page Source code
hapSim Man page Source code
haplin Man page Source code
haplinSlide Man page Source code
haplinStrat Man page Source code
haplinTDT Man page Source code
haptable Man page Source code
haptable.default Source code
haptable.gxe Source code
haptable.haplin Source code
haptable.haplinSlide Source code
haptable.haplinStrat Source code
lineByLine Man page Source code
lineConvert Source code
output Man page Source code
pQQ Man page Source code
pedToHaplin Man page Source code
plot Man page Man page Man page
plot.haplin Man page Source code
plot.haplinTDT Man page Source code
plot.haptable Man page Source code
plot.tdt Source code
postTest Source code
prepPed Man page Source code
print.HWE.test Source code
print.gxe Source code
print.haplin Man page Source code
print.haplinSlide Source code
print.haplinStrat Source code
print.haplinTDT Source code
print.info Source code
print.suest Source code
print.summary.haplin Man page Source code
print.summary.haplinTDT Source code
print.summary.tdt Source code
print.tdt Source code
rbindFiles Man page Source code
readData Source code
snpPos Man page Source code
snpPower Man page Source code
snpSampleSize Man page Source code
suest Man page Source code
summary.haplin Man page Source code
summary.haplinStrat Source code
summary.haplinTDT Man page Source code
summary.tdt Source code
summary.tri.glm Source code
tdt Source code
tdt.basic Source code
textlabel Source code
toDataFrame Man page Source code
uniqueID Source code

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
Haplin documentation built on May 29, 2017, 8:42 p.m.