Software

armitage

Armitage trend chi-square statistics to evaluate the association of a trait with SNP genotype predictors given a dose vector of length 3. Distributed for S-PLUS and R with special installation steps given in the README. Version 0.0.2, updated 1/17/2008.

• README.armitage
• armitage_R
• armitage_S

arp.gee

Simultaneously estimate a trait-locus position and its genetic effects for affected relative pairs by one of two methods. Either allow a different trait-locus effect for each ARP type, or constrain the trait-locus effects according to the marginal effect of a single susceptibility locus. We include a goodness of fit statistic for the constrained model. README and package sources provided for S-PLUS and R. Version 0.1.0, updated 4/2005.

• README.arp.gee
• arp.gee_R
• arp.gee_S

compositeLD

A method to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. README and package sources are provided for S-PLUS and R. Version 0.2.1, updated 12/2006.

• README.compositeLD
• compositeLD_R
• compositeLD_S

GASSOC Software

Statistical methods for genetic associations using cases and their parents. Last Updated 6/04/01

• README.gassoc
• GASSOC

haplo.stats

A suite of S-PLUS/R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The genetic markers are assumed to be codominant (i.e., one-to-one correspondence between their genotypes and their phenotypes). Version 1.4.0, updated 10/2008.

• README.haplo.stats
• User Manual
• haplo.stats_R
• haplo.stats_S

hwe

Test the fit of genotype frequencies to Hardy-Weinberg Equilibrium proportions for autosomes and the X chromosome. Different statistical tests are provided, as well as an option to evaluate statistical significance by either exact methods or simulations. README and package sources are provided for S-PLUS and R. Version 0.1.3, updated 1/17/2008.

• README.hwe
• hwe_R
• hwe_S

hweStrata

Calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. Written in the C programming language, available as executable for Windows and Unix, in addition to the source code. (Updated 11/2006)

• README.hweStrata
• User Manual
• Package Source

ibdreg

A package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. README and package sources are provided. Version 0.1.0, updated 12/2006.

• README.ibdreg
• ibdreg_R
• ibdreg_S

pedShrink

Trim a pedigree to specified bit size with priority placed on trimming uninformative subjects. Version 0.1.0. Updated 7/2008.

• README.pedShrink
• pedShrink_R

Division of Biomedical Statistics and Informatics Splus/R Extensions