HAPMIXMAP free download, HAPMIXMAP download on software download

You may use HAPMIXMAP to easily test all lociin a candidate gene in which tag SNPs have been typed in cases and controls HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies. It is mainly intended to model HapMap haplotypes using tag SNP genotype data. HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program developed by Scheet and Stephens (2006). The program models unphased genotype data on unrelated individuals, and fits a model in which linkage disequilibrium is generated by K independent Poisson arrival processes corresponding to K modal haplotype states. This corresponds to the observation that typically 2-4 common haplotypes account for most of the allelic diversity in any haplotype block, and that rarer haplotypes are typically slight variants of these modal haplotypes. The block-like structure of haplotypes in the genome, corresponding to ancestral recombination hotspots, is modelled by allowing the arrival rate to vary across the genome. This model is similar to that used in ADMIXMAP to model admixture between populations, and most of the code in HAPMIXMAP is derived from ADMIXMAP. The program generates the posterior distribution of haplotypes across each chromosome, given the observed unphased genotype data. Score tests for association with an outcome variable are constructed by averaging over this posterior distribution. For a binary outcome variable (as in a case-control study) the program fits a logistic regression model. For a quantitative trait, the program fits a linear regression model, and for survival-time data the program fits a Cox regression model. The program is intended to be used with HapMap genotype data: a dataset is available for a panel of 60 unrelated individuals in each of three continental groups. These genotype data can be combined with genotype data on the individuals under study (typically a case-control collection) at a subset of the HapMap loci. Usually this subset of HapMap loci will be tag SNPs such as those on the Affymetrix or Illumina arrays). The program then models the haplotype structure of the population, using data from both the HapMap panel and the individuals under study, and generates the posterior distribution of genotypes at all untyped HapMap loci in the individuals under study. Using HAPMIXMAP, any genetic association study using a panel of tag SNPs can be analysed as if all loci in the HapMap had been typed. The score test for association allows correctly for uncertainty in inference of the genotypes at untyped loci. It also yields, as a by-product, a measure of the efficiency of the study design in testing each locus, in comparison with a study in which the locus is typed directly). This is the ratio of observed to complete information in the score test. This can be used to evaluate the adequacy of a tag SNP panel, and to decide whether additional genotyping of untyped loci is likely to yield any extra information. hapmixmap requires R to be installed on your computer. R is a free statistical analysis program

HAPMIXMAP Related Software