Haplin is a free software package designed to analyze case-parent triad (trio) data and/or case-control data. Some of its main features are:
- Analyses of the case-parent triad design, the case-control design, and “hybrid” designs, i.e. combinations of case-parent triads and control-parent triads.
- Optimal use of designs with missing genotypic data, for instance if a single SNP has not been typed in some individuals, or when the case father has not been genotyped at all, or when the control parents are not available.
- Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data.
- Estimation of relative risk (RR) associated with each haplotype, not only significance testing.
- Optional estimation of effects of maternal haplotypes, particularly relevant to perinatal epidemiology.
- Estimation of RRs, haplotypes etc. also on the X chromosome, with models including dose-response and X-inactivation.
- Estimation of parent-of-origin (PoO) effects.
- Gene-environment (GxE) interactions can be estimated for all genetic effects
- For instance, estimation of PoO interactions with environmental exposure (PoOxE effects).
- Support for GWAS data and parallel processing.
- Extensive facilities for power calculations.
Also available from Blackwell