LINKMAP is a program for calculating location scores of one locus against a fixed map of other loci.
LINKMAP is used with the program UNKNOWN. The calling order is:
UNKNOWN
LINKMAP
The input files for this suite of programs are:
PEDFILE
DATAFILE
The output files are:
OUTFILE
STREAM
UNKNOWN produces temporary files called IPEDFILE and SPEEDFILE;
along with DATAFILE, these serve as input for LINKMAP.
These constants are the same as in MLINK.
The program-specific part of DATAFILE consists of a single line that contains the locus number (input order) to be varied (moving locus); a stopping value for the recombination fraction; and the number of points to be evaluated in an interval (gridsize). Evaluations are made by moving the "locus varied" within the interval between flanking markers, or to one or the other of the ending intervals in the map. The interval between the starting and ending recombination values is divided into equal portions so that the total number of evaluations is equal to gridsize. The program must be restarted with a different chromosome order to test other intervals.
For the outside interval on the left hand side of the map, the recombination will decrease automatically from the initial value to the final value; therefore, the final value should be smaller than the initial value. For other intervals, the recombination rate will increase from the starting value to the final value. In interior intervals, the recombination between the flanking markers is held constant (assuming Haldane's mapping function). If the final recombination rate specified in DATAFILE is greater than the total recombination in the interval, the latter figure determines the division.
As an example, consider a map of four fixed loci, with a fifth locus whose position is varied. The DATAFILE could have the form:
5 0 0
0 0.0 0.0 0
5 3 2 4 1 << locus order
(locus description)
0 0 << sex-difference, interference
0.5 0.1 0.05 0.15
5 0.0 10
The program will make 10 likelihood evaluations at equally spaced
intervals, with locus 5 moving from 0.5 to 0.0 recombination with
locus 3. Similarly:
5 0 0
0 0.0 0.0 0
3 2 5 4 1 << locus order
(loci description)
0 0 << sex-difference, interference
0.1 0.0 0.05 0.15
5 0.05 10
will result in 10 likelihood evaluations starting with 0.0
recombination between loci 5 and 2, and ending with 0.0 recombi-
nation between loci 5 and 4. (As a consequence of rounding
error, the final recombination may not be exactly 0.0.)
When the constant BYFAMILY is "true," likelihoods are given for each family in OUTFILE.
Comments:
LINKMAP permits the sex-difference option 1 (constant ratio of
female/male genetic distance). The option 2 (generalized sex-
difference) cannot be used when calculating location scores.
Interference is not allowed with the LINKMAP program.
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