Summary: select what pair combinations will be used No Arguments
If you have loaded more than two sibs in any of your sibships this command allows you to include the extra sibs in the analysis commands (all sibs are automatically included for phase information if parents are missing). When using 'all pairs', each pair is considered as an independent pedigree but a weight (2/num_affecteds) is factored in to counteract inflation of significance due to the statistical dependence among these pairs.
Simply type 'pairs used' and indicate which pair setting you would like to use:
sibpair:1> pairs used the current pair setting is: *first affected/phenotyped sibpair only* Possible pair options: 1. First pair of affected/phenotyped sibs 2. All independent pairs of affected/phenotyped sibs* 3. All pairs of affected/phenotyped sibs* 4. All pairs pf affected/phenotyped sibs-UNWEIGHTED Enter the index of the analysis you want to use [1]: 2
*"independent" pairs of sibs are created by taking the first sib paired with sibs 2...n (for a three-sib sibship this will mean the sharing for pairs 1-2 & 1-3 will be computed). Therefore, the results can be different if you rearrange the order of the sibship. "all" pairs are created by taking the first sib paired with sibs 2...n, the second sib paired with 3...n, etc. For a four-sib sibship this means the sharing for pairs 1-2, 1-3, 1-4, 2-3, 2-4 and 3-4 will be computed. The sibs are considered as part of a whole family when inheritance vectors are determined and then each pair is treated as a essentially a separate pedigree for the purposes of analysis.
You DO NOT need to re-scan for a change in the pair setting to take effect.
The default is to use the first pair of affected/phenotyped sibs.