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. 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".

Version: 7.3.1
Depends: R (≥ 3.5.0)
Imports: tools, mgcv, MASS, ff, rlang, methods
Suggests: knitr, Rmpi, ggplot2, testthat, rmarkdown
Published: 2024-02-08
DOI: 10.32614/CRAN.package.Haplin
Author: Hakon K. Gjessing [aut, cre], Miriam Gjerdevik [ctb] (functions 'lineByLine', 'cbindFiles', 'rbindFiles', 'snpPower', 'snpSampleSize', 'hapSim', 'hapRun', 'hapPower', 'hapPowerAsymp', and 'hapRelEff'), Julia Romanowska ORCID iD [ctb] (new data format, parallelisation, new documentation), Oivind Skare [ctb] (TDT tests)
Maintainer: Hakon K. Gjessing <hakon.gjessing at uib.no>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://haplin.bitbucket.io
NeedsCompilation: yes
Citation: Haplin citation info
In views: MissingData
CRAN checks: Haplin results


Reference manual: Haplin.pdf
Vignettes: Introduction: installing and citing Haplin
Reading and preparing the data
Running Haplin analysis
Running Haplin on cluster
Relative efficiency


Package source: Haplin_7.3.1.tar.gz
Windows binaries: r-devel: Haplin_7.3.1.zip, r-release: Haplin_7.3.1.zip, r-oldrel: Haplin_7.3.1.zip
macOS binaries: r-release (arm64): Haplin_7.3.1.tgz, r-oldrel (arm64): Haplin_7.3.1.tgz, r-release (x86_64): Haplin_7.3.1.tgz, r-oldrel (x86_64): Haplin_7.3.1.tgz
Old sources: Haplin archive


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