Summary: select NPL scoring function Argument: < 'pairs' or 'all' > Default: displays the current setting
The 'score' command allows the user to select the NPL scoring function to be used during analysis with the 'scan' command. These functions offer a measurement of the degree of sharing among affected individuals and are not dependent on the specific model proposed for the disease as the parametric LOD score is. The statistic reported will represent the deviation from Mendelian expectation observed and will roughly follow the normal distribution.
The 'pairs' function computes a score based on the degree of sharing among all pairs of affected individuals in a pedigree. This statistic is similar to those used in non-parametric sib-pair or APM analyses.
The 'all' function examines all individuals simultaneously and assigns a higher score when more of them share the same allele by descent. It is our experience in extensive simulations and analysis of real pedigree data that the 'all' statistic provides a more powerful test.