Software for genetic association analyses in case-parent triads,
case-control data (or combined case-parent control-parent triads), with
SNP haplotypes from candidate genes or GWAS data
Web page last updated: May 25, 2016
Most recent version: Haplin 6.0.1, uploaded to CRAN May 27, 2016
HAPLIN is free software written for the purpose of analyzing case-parent
triad (trio) data and/or case-control data. Some of the main features of
The models estimated by Haplin are described in detail 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.
- Analyses of the case-parent triad design, the case-control design, and
"hybrid" designs using combinations of case-parent triads and
- Optimal use of designs with missing genotypic data, for instance a
single SNP has not been typed for some individuals, or when the case
father has not been genotyped at all, or when the control parents are
- 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 in perinatal
- Estimation of RRs, haplotypes etc. also on the X chromosome, with
models including dose-response and X-inactivation.
- Estimation of parent-of-origin effects.
- Gene-environment interactions can be estimated for all genetic effects
- Support for GWAS data and parallel processing.
PDF version here.
Also available from Blackwell
new in this version of Haplin?
Some features high on the Wish
List for Haplin
Haplin is written by Hakon K.
Gjessing. Hilde-Gunn Bruu contributed to early versions of the
data reading and preparation parts. Rolv Terje Lie has contributed
with numerous useful and insightful suggestions, and inspired the
work from its beginning. Nguyen Trung Truc programmed the nice
external GUI for generating Haplin syntax. Øivind Skare has done
extensive testing and simulations with the more recent versions of
Haplin, and added a TDT test. Astanand (Anil) Jugessur has provided
very useful feedback from a user's perspective, and authored a
number of papers using Haplin. Miriam Gjerdevik has written
the functions lineByLine and convertPed to recode and modify very large
text files, cbindFiles and rbindFiles to merge very large text files, and
snpPower, snpSamplesize, and hapPower to compute power and sample size for
single SNP and haplotype analyses.
Please feel free to contact me at firstname.lastname@example.org,
with questions or bug reports.
Note: Although we have done
our best to avoid errors, the software is offered without
any warranties. We
cannot take responsibility for any problems or damages caused by
Cite: If you use Haplin in
your publications, please refer to the Annals of Human Genetics
paper above. In addition, typing citation(package = "Haplin") in R will give you the most recent reference to the Haplin R-library.
Haplin is written for use with the statistical software R. However, it is
easy to install and requires no previous knowledge of R. R can be downloaded
free of charge from The R Project for
Statistical Computing. For Windows users, a shortcut to the R
installation file is found here.
Haplin is implemented as a standard R library, and should run without
problems on all reasonably new R versions, for Windows, Linux or MAC.
To install Haplin in R:
Start R and type install.packages("Haplin")
Haplin will then be installed automatically over the
internet from the CRAN library.
To start using Haplin, use the R command library(Haplin).
Haplin is then loaded and ready for use.
NOTE: Every time you start a new R session you must load
Haplin with the R command
(However, you only need to install
it from CRAN once.)
Haplin is run by the single command
(or whatever the path to the data file is). The data file (data.dat)
can have any name, but should be a text file in a specific format
(see below). This command reads data, performs the estimation and
prints and plots the result in one run.
By default, Haplin excludes triads with missing data. To include
these triads in the calculations, include the use.missing argument:
use.missing = T)
(The letter "T" is short
for TRUE in R)
For more examples of how to run Haplin, see the haplin help file (in
R, type ?haplin). For a quick overview of all available functions in Haplin,
use help(package = "Haplin").
I have collected a few pieces of
advice that may be useful if you encounter problems.
The complete reference list of help files is here
There are three ways to handle input data with Haplin:
- The native Haplin data file format is a fairly simple ASCII
file, described here.
- If the data (on relatively few SNPs) are available in a standard
ped-format, it is possible to convert ped files directly to the Haplin
format. See here for details.
- With a larger number of SNPs in ped-format, such as a GWAS ped file
produced by plink, data can be read into Haplin via the GenABEL package
data format. A complete description of how to import and handle GWAS
data is found here.
To test that Haplin runs properly, you can download the trial data files HAPLIN.trialdata.txt and HAPLIN.trialdata2.txt,
Haplin with the commands
use.missing = T, maternal = T)
haplin("HAPLIN.trialdata2.txt", use.missing = T, n.vars = 2, ccvar = 2,
design = "cc.triad", reference = "ref.cat", response = "mult")
The results should look something like this: HAPLIN.trialrun.txt,
In addition, a plot is produced, which should look something
like this: HAPLIN.trialrun.jpg, HAPLIN.trialrun2.jpg.
easily accessible Graphical User Interface for generating Haplin
syntax is under development, and a preliminary versjon is available
at haplin.fhi.no, thanks to
Nguyen Trung Truc. The syntax generator helps setting up Haplin
commands which can be cut and pasted into your own R window. It
includes some (but not all) of the features currently available in
Model and estimation
The models implemented in Haplin are extensions of the log-linear
models described and developed in the papers
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. Wilcox AJ, Weinberg CR,
Lie RT (1998). Distinguishing the effects of maternal and offspring
genes through studies of "case-parent triads". American
Journal of Epidemiology, 148(9):
Weinberg CR, Wilcox AJ, Lie RT (1998). A log-linear approach to
case-parent-triad data: assessing effects of disease genes that act
directly or though maternal effects and that may be subject to
parental imprinting. American
Journal of Human Genetics, 62: 969-78
and follow-ups to these. The basic log-linear model for case-parent
triad data allows a user to compute relative risks associated with a
variant allele, together with corresponding confidence intervals and
p-values. It also allows a similar effect estimation for maternal
alleles, i.e. to study the effect of genes of the mother
that may influence the
development of the fetus. Haplin extends these models to situations
with multiple densely spaced SNPs (or other markers), where phase is
unknown. Haplin then estimates the relative risks associated with haplotypes,
not only single
markers. In addition, Haplin uses a parametrization that will detect
(at least with sufficient sample size) dominance- or recessive
deviations from a dose-response model. For some details about
parametrization, choice of reference category and interpretation of
results, see parametrization.pdf.
The most recent Haplin version also includes the option to run on
case-control data, or to combine case-parent triads with
Hakon K. Gjessing
Division of Epidemiology
Norwegian Institute of Public Health
P.O.Box 4404 Nydalen
N-0403 Oslo, NORWAY