mlink-pedin
ilink-pedin
linkmap-pedin
To get better protection against a crash, we can use an auxiliary program ckpt, but this is not for novices. See: FD: README.checkpoint.
Here is what the 3 final.out files will look like. First, mlink-final.out:
MLINK Pedigree File : pedin.tpd Parameter File : datain.tdt Output Pedigree File : pedfile.dat Output Parameter File : datafile.dat Log File : lsp.log Stream File : lsp.stm Date Run : 7-Nov-95 12:51:21 Sex Difference : 0 Recomb. Fraction to Vary : 1 Increment Value : 2.00000000 Stop Value : 1.00000000 Locus Order : 1 2 Male Recomb. Fractions : 0.00000000 Initial Recomb. Fraction : 0.01000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.05000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.10000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.20000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.30000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.40000000 Increment Value : 2.00000000 Stop Value : 1.00000000 LINKAGE (V5.1) WITH 2-POINT AUTOSOMAL DATA ORDER OF LOCI: 1 2 THETAS 0.500 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -19.273056 -8.370164 ----------------------------------- TOTALS -19.273056 -8.370164 -2 LN(LIKE) = 3.85461e+01 LOD SCORE = 0.000000 THETAS 0.000 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -100000000000000000000.000000 -43429355638650388480.000000 ----------------------------------- TOTALS -100000000000000000000.000000 -43429355638650388480.000000 -2 LN(LIKE) = 2.00000e+20 LOD SCORE = -43429355638650388480.000000 THETAS 0.010 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -21.145838 -9.183501 ----------------------------------- TOTALS -21.145838 -9.183501 -2 LN(LIKE) = 4.22917e+01 LOD SCORE = -0.813337 THETAS 0.050 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -19.701227 -8.556116 ----------------------------------- TOTALS -19.701227 -8.556116 -2 LN(LIKE) = 3.94025e+01 LOD SCORE = -0.185952 THETAS 0.100 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -19.223124 -8.348479 ----------------------------------- TOTALS -19.223124 -8.348479 -2 LN(LIKE) = 3.84462e+01 LOD SCORE = 0.021685 THETAS 0.200 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -18.986975 -8.245921 ----------------------------------- TOTALS -18.986975 -8.245921 -2 LN(LIKE) = 3.79740e+01 LOD SCORE = 0.124243 THETAS 0.300 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -19.055367 -8.275623 ----------------------------------- TOTALS -19.055367 -8.275623 -2 LN(LIKE) = 3.81107e+01 LOD SCORE = 0.094541 THETAS 0.400 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -19.200549 -8.338675 ----------------------------------- TOTALS -19.200549 -8.338675 -2 LN(LIKE) = 3.84011e+01 LOD SCORE = 0.031489
MLINK Pedigree File : pedin.tpd Parameter File : datain.tdt Output Pedigree File : pedfile.dat Output Parameter File : datafile.dat Log File : lsp.log Stream File : lsp.stm Date Run : 7-Nov-95 12:51:24 Sex Difference : 0 Recomb. Fraction to Vary : 1 Increment Value : 2.00000000 Stop Value : 1.00000000 Locus Order : 1 3 Male Recomb. Fractions : 0.00000000 Initial Recomb. Fraction : 0.01000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.05000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.10000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.20000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.30000000 Increment Value : 2.00000000 Stop Value : 1.00000000 Initial Recomb. Fraction : 0.40000000 Increment Value : 2.00000000 Stop Value : 1.00000000 LINKAGE (V5.1) WITH 2-POINT AUTOSOMAL DATA ORDER OF LOCI: 1 2 THETAS 0.500 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -12.459367 -5.411023 ----------------------------------- TOTALS -12.459367 -5.411023 -2 LN(LIKE) = 2.49187e+01 LOD SCORE = 0.000000 THETAS 0.000 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -100000000000000000000.000000 -43429355638650388480.000000 ----------------------------------- TOTALS -100000000000000000000.000000 -43429355638650388480.000000 -2 LN(LIKE) = 2.00000e+20 LOD SCORE = -43429355638650388480.000000 THETAS 0.010 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -14.332149 -6.224360 ----------------------------------- TOTALS -14.332149 -6.224360 -2 LN(LIKE) = 2.86643e+01 LOD SCORE = -0.813337 THETAS 0.050 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -12.887538 -5.596975 ----------------------------------- TOTALS -12.887538 -5.596975 -2 LN(LIKE) = 2.57751e+01 LOD SCORE = -0.185952 THETAS 0.100 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -12.409435 -5.389338 ----------------------------------- TOTALS -12.409435 -5.389338 -2 LN(LIKE) = 2.48189e+01 LOD SCORE = 0.021685 THETAS 0.200 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -12.173286 -5.286780 ----------------------------------- TOTALS -12.173286 -5.286780 -2 LN(LIKE) = 2.43466e+01 LOD SCORE = 0.124243 THETAS 0.300 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -12.241679 -5.316482 ----------------------------------- TOTALS -12.241679 -5.316482 -2 LN(LIKE) = 2.44834e+01 LOD SCORE = 0.094541 THETAS 0.400 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- 1 -12.386861 -5.379534 ----------------------------------- TOTALS -12.386861 -5.379534 -2 LN(LIKE) = 2.47737e+01 LOD SCORE = 0.031489
Notice that the Lod score for each candidate theta is shown. The Lodscore is the difference between the entry in the LOG 10 LIKE column for that theta and theta = 0.5. The large numbers are -infinity, indicating that theta cannot be 0, because there is an obligatory recombinant.
Now, let us see ilink-final.out:
ILINK Pedigree File : pedin.tpd Parameter File : datain.tdt Output Pedigree File : pedfile.dat Output Parameter File : datafile.dat Log File : lsp.log Stream File : lsp.stm Date Run : 7-Nov-95 12:51:32 Sex Difference : 0 Interference : 0 Locus Order : 2 3 Male Recomb. Fractions : 0.10000000 CHROMOSOME ORDER OF LOCI : 1 2 THETAS: 0.500 -2 LN(LIKE) = 3.38332e+01 LOD SCORE =-6.76864e-09 NUMBER OF ITERATIONS = 4 NUMBER OF FUNCTION EVALUATIONS = 11 PTG = -5.44302e-07
ILINK shows that the best estimate of theta between markers 2 and 3 is 0.5, so they are probably not on the same chromosome arm.
Finally, let us look at linkmap-final.out:
LINKMAP Pedigree File : pedin.tpd Parameter File : datain.tdt Output Pedigree File : pedfile.dat Output Parameter File : datafile.dat Log File : lsp.log Stream File : lsp.stm Date Run : 7-Nov-95 12:51:41 Sex Difference : 0 Test Locus : 1 Stop Value : 0.00000000 Number of Evaluations : 5 Locus Order : 1 2 3 Male Recomb. Fractions : 0.50000000 0.25000000 THETAS 0.500 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.899877 -10.813856 -2 LN(LIKE) = 4.97998e+01 THETAS 0.400 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.827371 -10.782367 -2 LN(LIKE) = 4.96547e+01 THETAS 0.300 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.682189 -10.719316 -2 LN(LIKE) = 4.93644e+01 THETAS 0.200 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.613797 -10.689613 -2 LN(LIKE) = 4.92276e+01 THETAS 0.100 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.849945 -10.792171 -2 LN(LIKE) = 4.96999e+01 THETAS 0.000 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -100000000000000000000.000000 -43429355638650388480.000000 -2 LN(LIKE) = 2.00000e+20 LINKMAP Pedigree File : = Parameter File : datain.tdt Output Pedigree File : pedfile.dat Output Parameter File : datafile.dat Log File : lsp.log Stream File : lsp.stm Date Run : 7-Nov-95 12:51:45 Sex Difference : 0 Test Locus : 1 Stop Value : 0.25000000 Number of Evaluations : 5 Locus Order : 2 1 3 Male Recomb. Fractions : 0.00000000 0.25000000 THETAS 0.000 0.250 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -100000000000000000000.000000 -43429355638650388480.000000 -2 LN(LIKE) = 2.00000e+20 THETAS 0.050 0.222 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.466375 -10.625589 -2 LN(LIKE) = 4.89327e+01 THETAS 0.100 0.187 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -23.994311 -10.420575 -2 LN(LIKE) = 4.79886e+01 THETAS 0.150 0.143 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -23.878945 -10.370472 -2 LN(LIKE) = 4.77579e+01 THETAS 0.200 0.083 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.098045 -10.465626 -2 LN(LIKE) = 4.81961e+01 THETAS 0.250 0.000 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -100000000000000000000.000000 -43429355638650388480.000000 -2 LN(LIKE) = 2.00000e+20 LINKMAP Pedigree File : = Parameter File : datain.tdt Output Pedigree File : pedfile.dat Output Parameter File : datafile.dat Log File : lsp.log Stream File : lsp.stm Date Run : 7-Nov-95 12:51:48 Sex Difference : 0 Test Locus : 1 Stop Value : 0.50000000 Number of Evaluations : 5 Locus Order : 2 3 1 Male Recomb. Fractions : 0.25000000 0.00000000 THETAS 0.250 0.000 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -100000000000000000000.000000 -43429355638650388480.000000 -2 LN(LIKE) = 2.00000e+20 THETAS 0.250 0.100 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.849945 -10.792171 -2 LN(LIKE) = 4.96999e+01 THETAS 0.250 0.200 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.613797 -10.689613 -2 LN(LIKE) = 4.92276e+01 THETAS 0.250 0.300 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.682189 -10.719316 -2 LN(LIKE) = 4.93644e+01 THETAS 0.250 0.400 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.827371 -10.782367 -2 LN(LIKE) = 4.96547e+01 THETAS 0.250 0.500 ----------------------------------- PEDIGREE | LN LIKE | LOG 10 LIKE ----------------------------------- TOTALS -24.899877 -10.813856 -2 LN(LIKE) = 4.97998e+01
To get lod scores compare the LOG 10 LIKE column entry for your candidate theta against the entry for theta = 0.5 (which means 1 is unlinked to both 2 and 3). This is the first and last entry in the output table.