LRP is an auxiliary program of the LINKAGE package. "LRP" stands for "Linkage Report Program".
LRP is used for reading stream.out output file which is created by LCP program (pedin shell script). See LCP howto.
LRP 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.
LRP command is:
lrp
Let's assume that 2-point linkage analysis was done using LCP. Required LRP input files are listed in LCP howto.
% lrp
l-------------------------------------------------k
x L I N K A G E R E P O R T P R O G R A M x
m-------------------------------------------------j
Input File and Report Title
--------------------------------
STREAM file name [stream.out] : stream.out
REPORT title [] :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Nothing to change here. Hit Page-Down.
l-------------------------------------------------k
x L I N K A G E R E P O R T P R O G R A M x
m-------------------------------------------------j
Report Options
--------------------------------
General pedigree reports : <-
Three-generation pedigree reports :
Experimental cross pedigree reports :
Full stream file reports :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Choose "General pedigree reports". Hit Page-Down.
l-------------------------------------------------k
x L I N K A G E R E P O R T P R O G R A M x
l-------------------------------------------------k
General Pedigree Report Options
--------------------------------
Two-point lodscore report (LODSCORE) :
Multi-point order report (ILINK) :
Location score report (LINKMAP) :
Lod table report (MLINK) : <-
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Choose "Lod table report (MLINK)", since we did 2-point analysis with MLINK in LCP howto. Hit Page-Down.
l-------------------------------------------------k
x L I N K A G E R E P O R T P R O G R A M x
l-------------------------------------------------k
Lod Table Report (MLINK) Formats
------------------------------------------
Table format : <-
Full format :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Choose "Table format". Hit Page-Down.
l-------------------------------------------------k
x L I N K A G E R E P O R T P R O G R A M x
l-------------------------------------------------k
Lod Table Report (MLINK) Options
-----------------------------------------
Display LOG 10 results [Yes] : Yes
Display LOG e results [No] : No
Include Pedigrees [No] : No
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Let's keep default settings. Hit Page-Down.
l-------------------------------------------------k
x L I N K A G E R E P O R T P R O G R A M x
l-------------------------------------------------k
Report Output Options
--------------------------------------
Output report to the screen : <-
Output report to a file :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit
Let's output results to screen. Hit Page-Down and results are shown:
L O D T A B L E R E P O R T
File: stream.out Screen: 1 of 1
------------------------------------------------------------------------------
Order 0.0 0.01 0.05 0.1 0.2 0.3 0.4
----- ------- ------- ------- ------- ------- ------- -------
1=2 -infini -140.40 -64.39 -34.86 -10.80 -1.88 0.58 a
1=3 -infini -193.17 -85.37 -43.68 -10.15 1.57 3.50 a
= = Test Interval
a = LOD Scores (LOG 10)
b = LOG 10 Likelihoods (LOG 10)
------------------------------------------------------------------------------
Enter Command :
CTRL/A - Abort CTRL/H - Help CTRL/Z - Exit CTRL/R - Return
Results can be also written to file, just choose "Output report to a file" from previous screen.
Order column shows which markers were tested. Example 1=2: test was done between locus 1 (disease locus) and locus 2 (marker 1), etc. Columns with headers 0.0, 0.1, etc. are recombination fractions (theta) between tested loci.
From this example we can see that highest 2-point lod score was 3.50 between disease locus (locus 1) and locus 3 (marker 2) and recombination fraction was 0.4.
Peter Cartwright
Handbook of Human Genetic Linkage, Joseph D. Terwilliger and Jurg Ott. Johns Hopkins University Press, Baltimore (1994)