Linkage Control Program (LCP) is used to generate a shell script (pedin) which runs some LINKAGE programs (ILINK, LINKMAP, LODSCORE, MLINK and UNKNOWN).
LCP is text-menu driven program and moving between screen is done by "Page-Down" and "Page-Up" keys and selecting different options is done with arrow keys.
LCP command is:
lcp
Input files are LINKAGE pedigree (pedin.dat) and locus (datain.dat) files.
Example of setting up 2-point linkage analysis with MLINK. Our input files are pedigree file (pedin.dat) and locus file (datain.dat). Pedigree file contains 2 multiallelic markers (locus 2 and 3) and one disease locus (locus 1).:
% lcp
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| L I N K A G E C O N T R O L P R O G R A M |
m---------------------------------------------------j
Input Files
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COMMAND file name [pedin] : pedin
LOG file name [final.out] : final.out
STREAM file name [stream.out] : stream.out
PEDIGREE file name [pedin.dat] : pedin.dat
PARAMETER file name [datain.dat] : datain.dat
Secondary PEDIGREE file name [] :
Secondary PARAMETER file name [] :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Our input files are corrent and let's use default values. Press "Page-Down" key go next screen.
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| L I N K A G E C O N T R O L P R O G R A M |
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Pedigree Options
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General pedigrees : <-
Three-generation pedigrees :
Experimental cross pedigrees :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Arrow show current selection. We have General pedigrees: Hit Page-Down.
l---------------------------------------------------k
| L I N K A G E C O N T R O L P R O G R A M |
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General Pedigree Analysis Options
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LODSCORE :
ILINK :
LINKMAP :
MLINK : <-
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Choose MLINK (use arrow keys) and hit Page-Down.
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| L I N K A G E C O N T R O L P R O G R A M |
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MLINK - Test Options
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Specific evaluation :
Lod score table :
Multiple pairwise Lod table : <-
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Choose "Multiple pairwise Lod table" (use arrow keys) and hit Page-Down.
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| L I N K A G E C O N T R O L P R O G R A M |
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MLINK - Sex Difference Options
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No sex difference : <-
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Choose "No sex difference " (well, not other options...eh) and hit Page-Down.
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| L I N K A G E C O N T R O L P R O G R A M |
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MLINK - Multiple Pairwise Lod Table Specification
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Command Screen
First locus set [] : 1
Second locus set [] : 2 3
Recombination fractions [.0] : .0
Other recomb. [.01 .05 .1 .2 .3 .4] : .01 .05 .1 .2 .3 .4
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
To "First locus set" field we input disease locus number, which is 1 on pedigree file. To "Second locus set" field we input marker loci 2 and 3, since we have only 2 marker loci on file. If you have example 10 marker loci on pedigree file and you want to analyze only 5 and 7, input only those marker in this field.
To "Recombination fractions" and "Other recomb." we leave as they are. Hit Page-Down.
l---------------------------------------------------k
| L I N K A G E C O N T R O L P R O G R A M |
m---------------------------------------------------j
Pedigree Options
--------------------
General pedigrees : <-
Three-generation pedigrees :
Experimental cross pedigrees :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
This screen it pretty confusing...you just set analysis, but you are back in Pedigree option screen? Well, this is okay, since in LCP one can set multiple different analysis in same pedin shell script. Now press CTRL-Z to exit LCP.
Next we run generated shell script
& pedin
Pedin script produces lot's of output to screen (output is from UNKNOWN and MLINK), here is example (scroll down to see more):
After analysis are done following files are created:
Next step is to use LCP to read stream.out file. See LRP howto!
Peter Cartwright
Handbook of Human Genetic Linkage, Joseph D. Terwilliger and Jurg Ott. Johns Hopkins University Press, Baltimore (1994)