Contents
This directory contains the C and C++ source files for SPLINK, TRANSMIT,
PED2SPL,
GH2STAT, and
SNPHAP.
It also contains
packages
for analysis of genetic association studies for the
STATA statistical system with some
exercises, and some
miscellaneous programs in the
R language.
Currently, the programs available are:
- SNPHAP,
a program for estimating frequencies of haplotypes of large
numbers of diallelic markers from unphased genotype data from
unrelated subjects
- Uses the EM algorith with "trimming" of improbable assignments
- Allows for missing data at some loci
- Can search for multiple solutions using random starting points
- Includes a Monte Carlo IP algorithm for multiple imputation, allowing
uncertainty of solutions to be explored
- STATA packages
- programs and exercises for genetic association studies
- programs for choosing "haplotype tagging" SNPs
- program for IBD regression (linkage analysis with covariates)
- programs for Monte Carlo permutation testing
- course materials for Advanced Statistical Modelling Course in the
Erasmus Summer Programme, 2002
- DGCgenetics, an R
package for analysis of genetic association studies, including some
practical exercises (this used to be called dgc.genetics
- Some extensions to the R
genetics package
- Several test data sets
- Miscellaneous teaching exercises
- snpMatrix, an R
package for analysis of genome-wide association studies. This is no
longer distributed from this site, but is now part of the
BioConductor project.
(http://www.bioconductor.org/)
The following packages are not maintained but are still available
on the site
- SPLINK, a program for sib
pair linkage analysis.
- Maximum likelihood subject to "possible triangle" restriction
- Marker haplotypes based on several closely linked markers
- Haplotype frequencies are estimated from the data
- TRANSMIT, a program for
transmission disequilibrium testing.
- Marker haplotypes based on several closely linked markers
- Parental genotype and/or haplotype phase may be missing
(There are a number of known
problems. In particular, the code for X loci is flawed)
- PED2SPL, a program for
interfacing of and marker selection from standard LINKAGE input files
to SPLINK and TRANSMIT.
- select specified markers from larger record
- old "binary" coding of marker genotypes handled
as well as the more modern numeric coding
- GH2STAT,
a program for processing IBD distribution files dumped by
genehunter, for later analysis in statistics packages.
- writes a record for each pair of pedigree members considered
- pairs may be restricted to be both affected and/or to have IBD
status which is a priori uncertain
- covariate and other data from the genehunter pedigree input file
may also be included in the output file
- output file is formatted for input into SAS, Splus or R, Stata, or
spreadsheet programs
The following package has been removed:
- TDTHAP, a package for TDT
with extended haplotypes in the "R" language.
For license and copying details, please see the LICENSE file.
Wider use of these programs is bound to throw up errors.
Programs other than those which must be run within Stata were written for
a Unix environment. On Microsoft Windows platforms, the easiest way to
implement them is by using
Cygwin,
which emulates Unix and includes the necessary compilers etc.
The files listed below - which are compressed groups of files -
have had their names and line-endings tweaked to suit either UNIX or PC
users.
- *.tar.gz files are targetted at UNIX users
- *.zip files are targetted at PC users
Please see the INSTALL file for further details.
David Clayton