FastMap
FastMap is a tool for genome wide association mapping that is designed for ‘Genetical Genomics’ studies using data from gene expression microarrays. While existing mapping tools are adept at handling a small number of phenotypes, they are quickly overwhelmed when the number of phenotypes rises into the thousands, as occurs with gene expression data. Further, with the developments in high throughput genotyping technology producing SNP data for millions of marker locations, many conventional association mapping tools bog down with even one phenotype. FastMap is designed to calculate the association between thousands of genes (or other phenotypes) and millions of SNPs in a reasonable amount of time on a standard desktop computer. Statistical significance is determined empirically using permutation testing. We exploit the similarities between SNPs to reduce the time complexity of the association mapping calculations at each marker. FastMap can accept both inbred mouse data, generally consisting of homozygous allele calls, and human SNP data, which includes heterozygous allele calls.
More information about FastMap can be found at http://cebc.unc.edu/fastmap.html.