Allele numbers -> binary factors

Mr J. Attwood jattwood at crc.ac.uk
Tue Dec 8 10:00:05 EST 1992


> Stephen Wood <swood at unixg.ubc.ca>
> writes to ask:
>
> The conversion programme I have that converts LINKAGE files to CRIMAP files
> seems to require the LINKAGE pedfile to be coded as binary factors.  I
> have received a pedfile by email coded as allele numbers.  Do you know
> of a program that can convert this to binary factors?  If not can you
> suggest any fix, short of re-entering the data?

I have written programs in C which read LINKAGE input files in numbered
allele format and write them out in a form suitable for either CRIMAP or
MAPMAKER. They do assume that the LINKAGE files were written by the EUROGEM
database software and have the probe and enzyme name as comments in the
parameter file, but this would be easy to fix. The programs will compile
under ULTRIX, SunOS 4.1.1 and MS-DOS (Turbo C v2). I could post the source
if this would do (or email it to interested parties), or supply a small number
of people with ready-compiled executables. The programs are fairly new and
haven't been exhaustively tested, but appear to work OK. The executables
test whether they were called as LINK2CRI or LINK2MAP and make the appropriate
translation - on Unix/Ultrix systems only one executable is required, with a
link to the alternative name; MS-DOS doesn't support links, so two differently
named versions of the executable are needed (and MS-DOS 3.0 or greater). One
extra file containing a list of aliases (short names, D-numbers, etc) for each
of the markers is required; these aliases end up in the output file so that
CRI-MAP and MAPMAKER will use D77X13487 instead of XXTTYYG/HinfI.

John Attwood,
MRC Human Biochemical Genetics Unit,
UCL,
4 Stephenson Way,
London NW1 2HE
UK

j.attwood at mrc-hbgu.ucl.ac.uk



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