HIV molecular immunology database
This tool takes a series of tab-delimited HLA types and returns any linkage disequilibrium found by a Fisher's exact test. For more information, see details below, and try Sample Input.
This program expects a list of HLA Class-I alleles. Each line of the input should be a unique patient ID followed by a list of HLAs, all separated by spaces or tabs. Missing data may be omitted, or indicated by a dash '-'.
HLA frequencies can be counted two different ways, which differ in how homozygous alleles are counted.
HLA type are reported with various resolutions (2, 4 or more digits). This tool provides three options for handling this.
In the results, the contingency table (column C) reports the number of subjects in each population with and without the given HLA. For each HLA, the tool computes the 2-sided exact Fisher's p-value, which represents the probability that the observed difference is due to chance. To correct for the false discovery rate caused by the calculation of multiple p-values, Storey's q-value is also provided (Storey JD: A direct approach to false discovery rates. J R Statist Soc B 2002, 64:479-498).