Summary: two locus TDT Argument: < offset between markers to examine > Default: analyze adjacent markers (offset=1)
The 'tdt2' command computes the two-locus version of the TDT. The identical rules for counting transmissions and non-transmissions are employed and as in the standard single marker TDT. If an offset is provided as an argument, the analysis will be done on pairs of markers as follows (1 and 1+offset, 2 and 2+offset, 3 and 3+offset, etc.). By default, offset is set to 1 so with no argument specified, 'tdt2' will produce a two-locus TDT test for marker pairs in map order (1 and 2, 2 and 3, 3 and 4, etc.) By nature, this model assumes there is no recombination between adjacent markers (or at least not a significant amount) which would interfere with the detection of potential founder haplotypes. Therefore it is probably most useful on closely spaced markers and/or in more recently founded populations. This command is only available after the 'tdt' analysis of a pedigree file.