The SCORE-nn.ALL file contains the location scores found by combining the results from all the input pedigrees. It also lists the maximum score found within each individual pedigree. The SCORE-nn.mmm files contain all the location scores computed within each original pedigree. Creation of the latter files is controlled through batch item #41. All these location scores are given in log10 units and are directly comparable to multipoint LOD scores. The scores are listed by total genetic distance from the first marker, in cM.
The degree of locus heterogeneity is commonly measured by alpha, defined as the a priori portion of pedigrees linked at a location, i.e., if there is a trait locus in the region, alpha is the proportion of these pedigrees that contains an affected genotype at this trait locus.
The overall parametric linkage analysis results are now always reported in two ways: (1) for alpha = 1.0 (i.e., assumming no locus heterogeneity) and (2) maximized over a grid of alpha values: 0.00, 0.05, 0.10, ..., 0.90, 0.95, 1.00. In addition, if an alpha value less than 1.0 is specified in batch item #13.2, then several more results are listed. These additional results include for each pedigree and each position the posterior probability that that pedigree is one of the linked pedigrees, given the selected value for alpha. This enables one to separate the linked and unlinked pedigrees in an unbiased fashion.
The SOFAR-nn.OUT file contains, in a form suitable for rerunning this program with additional pedigrees, the total location scores found up to the last completed pedigree, i.e., the partial results so far.
The STATS-nn.mmm files contain for each original pedigree the empirical p-value for each of five non-parametric linkage statistics, evaluated at each marker. This p-value is a conservative estimate of the true p-value. Also in this file is a table of -log10(p-values) suitable for graphing.
The STATS-nn.ALL file contains the overall results of these five statistics, i.e., the p-values derived by combining the results from all the pedigrees. Also in this file is a table of -log10(p-values) suitable for graphing.
For a detailed description of the five statistics shown, please see Lange and Lange (2004), Sobel and Lange (1996), and Whittemore and Halpern (1994) listed in the References section.