LODSCORE is one of the options of LINKAGE (LCP). LODSCORE allows you to find two point lodscores for your markers. Before you run LCP, make sure you have the following files in your directory:
- A Recoded *.ped File
- The datain.dat File
These step-by-step instructions will guide you through the program. On the left side of the table are instructions and on the right is what should appear on your screen. Typed commands are in bold text.
1. At the user prompt, type lcp. Press (RETURN) user@humgen% lcp 2. A screen entitled LINKAGE CONTROL PROGRAM will appear. On this screen, you must specify the input files for the program. Use the arrows on your keyboard to move up and down the list. Use the (DELETE) key when editing information in LCP. DO NOT USE THE BACKSPACE KEY. If you accidentally use the wrong key, you will end up on another screen. Just hit backspace unitl you return to the right screen. Change the PEDIGREE file name to the file name of your recoded data. The default PARAMETER file name is usually correct. Make sure it matches the name of your datain.dat file (if you named it something other than datain.dat). In this example, r-pedigree1.ped is used.
After you are finished, press (CTRL) N
COMMAND file name [pedin] :
LOG file name [final.out] :
STREAM file name [stream.out] :
PEDIGREE file name [pedin.dat] :
PARAMETER file name [datain.dat] :
Secondary PEDIGREE file name [] :
Secondary PARAMETER file name [] :pedin
final.out
stream.out
r-pedigree1.ped
datain.dat
3. At the Pedigree Options screen select General Pedigrees. Press (CTRL) N
General pedigrees :
Three-generation pedigrees :
Experimental cross pedigrees :<- 4. At the General Pedigree Analysis Options screen, choose LODSCORE. Press (CTRL) N
LODSCORE :
ILINK :
LINKMAP :
MLINK :<- 5. At the Sex Difference Options screen, choose the oppropriate option. Press (CTRL) N
No sex difference :
Varying sex difference :<- 6. Next, you will arrive at the Command Screen. Here, you must specify loci pairs for lodscoring. To do this, set the first locus to 1 (the disease locus). Then, set the second loci as all of your markers by pressing (CTRL) O. When you are finished, press (CTRL) N
First locus set [] :
Second locus set [] :
Male recombination fraction [.1] :1
p1 p2 p3 p47. You should be back at the screen you saw in step 3 (Pedigree Options). Now you are finished entering the parameters for the LODSCORE program. Press (CTRL) Z to return to the user prompt.
General pedigrees :
Three-generation pedigrees :
Experimental cross pedigrees :<- user@humgen%
The next step is to run the pedin program. The pedin program will use all the specifications you entered in the LCP program to calculate two-point lodscores for your data. At the user prompt, type the command pedin. If this does not work, type ./pedin. Press (RETURN). The screen will fill up with a series of data sets that look something like this:Number of alleles at locus 1 is 2
Number of alleles at locus 2 is 4
The number of haplotypes used is 8
Maxcensor canbe reduced to -32767
ITERATION 1 T = 0.100 NFE = 2 F = 6.1340e+01
ITERATION 1 T = 0.012 NFE = 2 F = 6.1340e+01
ITERATION 1 T = 4.000 NFE = 2 F = 6.1340e+01
ITERATION 1 T = 1.000 NFE = 2 F = 6.1340e+01
loci 1 3
Now you can view lodscores with the Linkage Report Program. This program interprets the output of the pedin program. It allows you to see the two-point lodscores in a simple format.
1. At the user prompt, type lrp. Press (RETURN) user@humgen% lrp 2. A screen entitled LINKAGE REPORT PROGRAM will appear. On this screen, you can create a title for the report. Use the arrows on your keyboard to move up and down the list. Use the (DELETE) key when editing information in LRP. DO NOT USE THE BACKSPACE KEY. If you accidentally use the wrong key, you will end up on another screen. Just hit backspace unitl you return to the right screen. Do not change the default setting for STREAM file name. Type in the title you wish to give the report (optional). After you are finished, press (CTRL) N
STREAM file name [stream.out] :
REPORT title [] :stream.out
Pedigree One3. At the Report Options screen select General pedigree reports. Press (CTRL) N
General pedigree reports :
Three-generation pedigree reports :
Experimental cross pedigree reports :
Full stream file reports :<- 4. At the General Pedigree Report Options screen, choose LODSCORE. Press (CTRL) N
Two-point lodscore report (LODSCORE) :
Multi-point order report (ILINK) :
Location score report (LINKMAP) :
Lod table report (MLINK) :<- 5. Select a format. In this example, the table format will be used. Press (CTRL) N
Table format :
Full format :<- 6. At the Report Output Options screen, you may chose to just view the data or save it to a file. Since it is possible to return to this screen after viewing the data, select Output report to the screen. Press (CTRL) N
Output report to the screen :
Output report to a file :<- 7. The two-point lodscore report should now appear on your screen. To save this report to a file, press (CTRL) R. This will take you back to the Report Output Options screen. Select Output report to a file and press (CTRL) N. Create a report file name (the default is report.txt) and leave all the other default settings unchanged. Press (CTRL) N. You will return to the Report Output Options screen again. Press (CTRL) Z to exit the program.
T W O - P O I N T L O D S C O R E R E P O R T
File: stream.out Pedigree One Screen: 1 of 1
_____________________________________________
Order Recomb Lodscore
---------------------------------
1-2 0.4020 0.02
1-3 0.7660 0.11
1-4 0.1000 0.00
You should now have a *.txt file in your directory. This file can be edited in emacs. To print the file, at the user prompt type the command lpr followed by the name of the *.txt file.