On Thu, 1 Aug 2002, Carlos Enriqe Carleos Artime wrote:
> > > > Fine. Could you perhaps make some comments for Debian-Med or should we just > > copy this description to > > > > http://www.debian.org/devel/debian-med/microbio > > Ups, I'm not a Debian developer (yet...), so I would need first a > sponsor for the package. > > Anyway, I'm not fluent in English, so I quote here some paragraphs > from Loki's documentation just in case they are useful: > > -------------------------------------------------------------- > > The programs described here are an implementation of the methods > described in S.C. Heath (1997) "Markov chain Monte Carlo segregation > and linkage analysis for oligogenic models", > Am. J. Hum. Genet. 61:748-760, for MCMC analysis of quantitative > traits. The programs are intended for performing multipoint linkage > analyses on large, possibly complex, pedigrees. In contrast to > `normal' linkage packages, the exact penetrance model and even the > number of QTL affecting the trait do not have to be specified "a > priori". Joint estimation of QTL number, position, and effects is > possible, avoiding the problems that can arise from mis--specification > of these parameters. It should be noted that although the aims are > the same as with traditional linkage packages, the operation of the > programs and (more importantly) interpretation of the output are very > different. This program does *not* produce LOD scores - if you only > want LOD scores then you should look elsewhere. One reason for this > is that the LOD score approach is less flexible than the one used > here, particularly when models with multiple trait loci are > considered. The other reason is that LOD scores are computationally > costly (and tricky) to reliably estimate using MCMC. The approach > used here is to estimate the posterior probability for any given > chromosome region of at least 1 trait locus being in that region (and > possibly over a given size threshold). > > It is also possible to perform affected only IBD sharing analyses. > Although the same programs are used as for the parametric analyses, > the way the output is interpreted is quite different. In addition, it > is also possible for Loki to estimate the pairwise realized kinship > coefficients (i.e. the kinship coefficients for all pairs in the > pedigree at particular genomic positions conditional on linked > markers). These are currently not used by Loki, though in the future > it is planned to use this mechanism for implementing variance > component approaches for linkage mapping. Loki has been used to > produce kinship coefficient matrices for variance component analyses > using external programs (Visscher PM, Haley Cs, Heath SC, Muir WJ, > Blackwood DHR, 1999, "Detecting QTLs for uni- and bipolar disorder > using a variance component method", Psych. Genet. 9:75-84). > > There are two main programs, Prep and Loki, which respectively > handle data input and the MCMC analysis. The data preparation > program, Prep, reads in data from a wide variety of input formats, > tests for consistency of pedigree and marker data, recodes the data, > and outputs standardized binary files for the analysis program, Loki. > Also included in the package are several small programs and scripts > which help in the interpretation of the output from Loki. > > Also included with the loki_2.3 distribution is a small collection of > short programs and perl scripts which I use to help analyze the output > from Loki. These are included in the hope that they might be of use > to other people. Feedback on the scripts (and on Loki as a whole) is > welcome. If the scripts prove useful then they might be expanded to > fit with people's requirements. > > Simon C. Heath > > -------------------------------------------------------------------- > > > > > > I think includion into med-bio meta package would make sense. > > > > Kind regards > > > > Abdreas. > > > > > > The package includes at present a routine with a non-profit license, > that makes it non-free (med-bio-contrib?). Upstream author (Simon > Heath) told me that he has already replaced that routine by one of his > own. So the next release of the program, coming soon, will be > completely free according to the DFSG. > > Cheers, > > carleos >
