LOD score too high - answers
Daniel E. Weeks
dweeks at WATSON.HGEN.PITT.EDU
Thu Feb 9 14:59:25 EST 1995
On Thu, 9 Feb 1995, David Curtis wrote:
> To test the hypothesis of all linked against none
> linked you'd have 1 - 0.0 - 2 - 0.0 - 3 against 1 - 0.5 - 2 - 0.5 - 3, which
> would mean changing two intervals simultaneously.
Unfortunately, this is exactly what LINKMAP does when it computes
Ott's generalized lod score (which is described in his book). I think
this may be identified only as a lod score in the LRP output, but in the
final.out text output, it is identified as Ott's generalized lod score
(without further explanation). LINKMAP should compute multipoint lod
scores, but it cannot since it only does one order at a time.
For example, if 1 is the trait locus, and our given marker map is
2---0.05---3, then the multipoint lod score for the order
2---0.0---1---0.05---3 requires computation of two likelihoods:
A) The likelihood under order 2---0.0---1---0.05---3
B) The likelihood under order 1---0.5---2---0.05---3 (i.e., with the
trait off the map).
Thus, post-processing of LINKMAP output is required to compute valid
multipoint lod scores. I believe Jurg Ott distributes a utility
program to do this. I have one as well, which is now available in the
file 'map.tar.Z' by anonymous ftp from watson.hgen.pitt.edu. Please note
that my conversion program requires that you start each group of LINKMAP
runs with the trait locus off the marker map on the left.
I hope this helps clarify matters.
-- Dan Weeks --
Daniel E. Weeks, Ph.D.
The Wellcome Trust Centre Department of Human Genetics
for Human Genetics University of Pittsburgh
University of Oxford Crabtree Hall, Room A310
Windmill Road 130 DeSoto Street
Oxford OX3 7BN Pittsburgh, PA 15261
(+44) 865 742 441 (1-412) 624-3066
FAX: (+44) 865 742 196 FAX: (1-412) 624-3020
daniel.weeks at well.ox.ac.uk dweeks at watson.hgen.pitt.edu
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