LINKAGE/FASTLINK
program calculates LOD scores
for each chosen value of recombination fraction and
for each pedigree. This huge LOD score table is 3
dimensional (marker, recombination fraction, and family),
and can be hard to read. We have a Perl script which
for a fixed marker, scan the other two dimensions
to rank the LOD score for each pedigree.
set up
A "final.out" file has already been generated by
two-point analysis using the LINKAGE/FASTLINK program.
Note that in LINKAGE convention, locus 1 is the disease
locus (virtual), the first marker is locus 2. So a line
in the final.out file with "Locus Order : 1 2" is a linkage
analysis of the first marker (locus 2).
The parsing of the "final.out" crucially depends
on the rigid format such as the line like "Locus Order .... : 1 7".
This is a companion page for
W Li, F Haghighi, "Perl as a tool for linkage analysis",
American Journal of Human Genetics, supplement to vol 65,
page A260 (1999) (poster number 1452 at the
Annual Meeting of American Society of Human
Genetics 1999, San Francisco, CA)
