#set vir 1 set prompt off echo echo ===================================== echo Regression testing suite for Sib-pair echo This version: 2011-Feb-02 echo ===================================== echo set ple -1 echo echo Testing printing and output: echo echo ======== echo Test 1 echo ======== echo echo echo ABCDE echo Expect ABCDE echo ABCDE echo echo ======== echo Test 2 echo ======== echo echo echo \\{ A \\}\\n B echo Expect \{ A \} echo Expect B echo \{ A \}\nB echo echo ======== echo Test 3 echo ======== echo echo 1+1 echo Expect 2. 1+1 echo echo ======== echo Test 4 echo ======== echo echo "1+1" echo Expect 10.0 "1+1" echo echo ======== echo Test 5 echo ======== echo echo "1-2" echo Expect 0.01 "1-2" echo echo ======== echo Test 6 echo ======== echo echo "1 1" echo Expect 11 "1 1" echo echo ======== echo Test 7 echo ======== echo echo 1+"a/a" echo Expect b/b 1+"a/a" echo ======== echo Test 8 echo ======== echo echo 1d---2 echo Expect 3.0 1d---2 echo echo ======== echo Test 9 echo ======== echo echo ABCDE echo Expect ERROR: token "ABCDE" not recognised. ABCDE echo echo ======== echo Test 10 echo ======== echo echo 5.0E+04 echo Expect 50000. 5.0E+04 echo echo Testing arithmetic: echo echo ======== echo Test 11 echo ======== echo macro r=94906267 macro p=(%r - 2) macro q=(%r - 1) echo -log (abs (((%q + sqrt (%q * %q - %p * %r )) / %p - 1)- 2/%p)) / log(2) echo Expect 26.4999999... -log (abs (((%q + sqrt (%q * %q - %p * %r )) / %p - 1)- 2/%p)) / log(2) echo echo Similar in Scheme (complicated by q*q and p*r being exactly echo representable as long integers ie q*q-p*r is 0 if 64 bit float echo or 1 if 64 bit integers) echo eval (define r 94906267) eval (define p (- r 2)) eval (define q (- r 1)) eval (/ (- (log (/ (abs (- (- (+ q (sqrt (- (* q q) (* p r))) p) 1) (/ 2 p)))))) (log 2)) macro minpos = "4.94065646-324" echo echo (%minpos+%minpos)/%minpos echo Expect 2.0 (%minpos+%minpos)/%minpos eval (define minpos 4.94065646e-324) eval (/ (+ minpos minpos) minpos) echo echo Testing functions: echo macro xx=1.3 macro yy=0.6 echo echo ======== echo Test 12 echo ======== echo echo abs(log(%xx)/log(10.)-log10(%xx)) echo Expect ~ eps (usually 2.22E-016) abs(log(%xx)/log(10.)-log10(%xx)) echo echo ======== echo Test 13 echo ======== echo echo abs(tan(%xx+%yy)-(tan(%xx)+tan(%yy))/(1-tan(%xx)*tan(%yy))) echo Expect ~ eps (usually 2.22E-016) abs(tan(%xx+%yy)-(tan(%xx)+tan(%yy))/(1-tan(%xx)*tan(%yy))) echo echo ======== echo Test 14 echo ======== echo echo abs(asin(sin(%xx))-%xx) echo Expect 0.0 abs(asin(sin(%xx))-%xx) echo echo ======== echo Test 15 echo ======== echo echo abs(acos(cos(%xx))-%xx) echo Expect 0.0 abs(acos(cos(%xx))-%xx) echo echo ======== echo Test 16 echo ======== echo echo abs(atan(tan(%xx))-%xx) echo Expect 0.0 abs(atan(tan(%xx))-%xx) echo echo Testing date utilities: echo echo ======== echo Test 17 echo ======== echo echo julian 19700101 echo Expect 0.0 julian 19700101 echo set epoch julian set epoch julian echo julian 19700101 echo Expect 2440588 julian 19700101 echo echo ======== echo Test 18 echo ======== echo echo int((julian 20070416 - julian 19651204)/365.25) echo Expect 41 int((julian 20070416 - julian 19651204)/365.25) echo echo Testing statistical and genetic utilities: echo echo Expected results usually from the equivalent R command echo echo ======== echo Test 19 echo ======== echo echo pnorm {-20 -15 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 15 20} echo Expect [1] 1.0000000000000000000e+00 1.0000000000000000000e+00 echo Expect [3] 1.0000000000000000000e+00 1.0000000000000000000e+00 echo Expect [5] 9.9999999999999933387e-01 9.9999999999872013490e-01 echo Expect [7] 9.9999999901341229958e-01 9.9999971334842807646e-01 echo Expect [9] 9.9996832875816688002e-01 9.9865010196836989653e-01 echo Expect [11] 9.7724986805182079141e-01 8.4134474606854292578e-01 echo Expect [13] 5.0000000000000000000e-01 1.5865525393145704647e-01 echo Expect [15] 2.2750131948179208585e-02 1.3498980316300945772e-03 echo Expect [17] 3.1671241833119924327e-05 2.8665157187919391185e-07 echo Expect [19] 9.8658764503769809052e-10 1.2798125438858351639e-12 echo Expect [21] 6.2209605742717848604e-16 1.1285884059538407827e-19 echo Expect [23] 7.6198530241605269199e-24 3.6709661993127508291e-51 echo Expect [25] 2.7536241186062337371e-89 pnorm {-20 -15 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10 15 20} echo echo ======== echo Test 20 echo ======== echo echo pch { 1 3 12 20 43 100 200 } 2 echo Expect [1] 6.065307e-01 2.231302e-01 2.478752e-03 4.539993e-05 4.599055e-10 echo Expect [6] 1.928750e-22 3.720076e-44 pch { 1 3 12 20 43 100 200 } 2 echo echo ======== echo Test 21 echo ======== echo echo pch { 1 3 12 20 43 100 200 } 2 ncp 3 echo Expect [1] 8.781745e-01 6.215002e-01 6.345203e-02 5.180278e-03 1.394612e-06 echo Expect [6] 1.659037e-16 pch { 1 3 12 20 43 100 200 } 2 ncp 3 echo echo ======== echo Test 22 echo ======== echo echo qch { 6.065307e-01 2.231302e-01 2.478752e-03 4.539993e-05 4.599055e-10 1.928750e-22 3.720076e-44 } 2 echo Expect 1 3 12 20 43 100 200 qch { 6.065307e-01 2.231302e-01 2.478752e-03 4.539993e-05 4.599055e-10 1.928750e-22 3.720076e-44 } 2 echo echo ======== echo Test 23 echo ======== echo sml 0.17 0.21 0.08 0.03 echo echo ======== echo Test 24 echo ======== echo grr 0.1 0.2 0.1 case echo echo ======== echo Test 25 echo ======== echo tet 0.1 {1.1 1.2 1.5 2 3 4 5 6 7 10} echo echo ======== echo Test 26 echo ======== echo ito 0.01 0.5 0.5 0.0 echo echo Testing logical and comparative operations: echo echo ======== echo Test 27 echo ======== echo echo 1 == 1.0d0 echo Expect 1.0 1 == 1.0d0 echo echo ======== echo Test 28 echo ======== echo echo 1 ^= 1.0d0 echo Expect 0.0 1 ^= 1.0d0 echo echo ======== echo Test 29 echo ======== echo echo "a/a" == "a/a" echo Expect 1.0 "a/a" == "a/a" echo echo ======== echo Test 30 echo ======== echo echo "a/a" == "a/b" echo Expect 0.0 "a/a" == "a/b" echo echo ======== echo Test 31 echo ======== echo echo "a/a" ^= "a/b" echo Expect 1.0 "a/a" ^= "a/b" echo echo ======== echo Test 32 echo ======== echo echo "a/a" ^= "a/a" echo Expect 0.0 "a/a" ^= "a/a" echo echo ======== echo Test 33 echo ======== echo echo "a/a" < "a/a" echo Expect 0.0 "a/a" < "a/a" echo ======== echo Test 34 echo ======== echo "a/a" < "a/b" echo Expect 1.0 "a/a" < "a/b" echo echo ======== echo Test 35 echo ======== echo echo "a/a" > "a/b" echo Expect 0.0 "a/a" > "a/b" echo echo Testing string searches: echo clear set seeds 12345 12345 12345 read ped inline a with x x x alia were x x x are viewed x x x as variables x x x at up x x x be top x x x between to x x x Both they x x x bottom then x x x but the x x x cannot than x x x ceiling strongly x x x combined strong x x x originally pile x x x pile originally x x x strong combined x x x strongly ceiling x x x than cannot x x x the but x x x then bottom x x x they Both x x x to between x x x top be x x x up at x x x variables as x x x viewed are x x x were and x x x with a x x x ;;;; run echo echo ======== echo Test 36 echo ======== echo set echo on print ped a set echo off echo echo ======== echo Test 37 echo ======== echo set echo on print ped *h set echo off echo echo ======== echo Test 38 echo ======== echo set echo on print ped *h* set echo off echo echo ======== echo Test 39 echo ======== echo set echo on print ped * id a.. set echo off echo echo ======== echo Test 40 echo ======== echo set echo on print ped * id *i*i*l set echo off echo echo ======== echo Test 41 echo ======== echo set echo on select id a* b*t* w* set echo off wri clear # # Recoding # echo echo Testing data recoding: echo set loc a mar set loc b qua read cases inline 1 A/B 21.3 2 1/2 123 3 B/C 1 4 2/4 1.00001 5 D/3 99 ;;;; run write recode a 1 2 3 D to A B C x recode b 1 123 to 42.42 set nde 10 5 echo echo ======== echo Test 42 echo ======== echo write set nde 9 4 clear # # File manipulation etc # echo echo Testing file manipulation etc: echo set seeds 12345 12345 12345 set loc a mar read cases inline 1 x/x 2 A/A 3 A/B 4 B/B 5 x/x ;;;; run set loc b qua output update.dat echo # echo # Example update dataset echo # echo ped id b a z echo 1 1 1 C/C 9 echo 2 2 2 C/C 9 echo # echo # Person 3 echo # echo 3 3 3 A/B x echo 4 4 4 B/B x echo 5 5 5 C/C 9 echo 6 6 6 Z/Z 9 output echo echo ======== echo Test 43 echo ======== echo echo Contents of Update file: file cat update.dat echo echo ======== echo Test 44 echo ======== echo echo Original file echo write update a update.dat echo echo ======== echo Test 45 echo ======== echo echo After updating a echo write update a b update.dat echo echo ======== echo Test 46 echo ======== echo echo echo After updating a and b echo write set loc z qua update z update.dat echo echo ======== echo Test 47 echo ======== echo write file delete update.dat clear echo echo Pedigree rewriting, subpedigree and nuclear: echo ======== echo Test 48 echo ======== echo set twin mzdz merlin set loc mzdz qua read pedigree inline 1 1 3 4 m 1 1 2 3 4 m 1 1 5 7 4 m 2 1 6 8 4 f 2 ;;;; run write subpedigree write echo echo File compression: echo echo echo ======== echo Test 49 echo ======== echo ! output data.txt echo C echo B echo A output $ gzip data.txt echo echo ======== echo Test 50 echo ======== echo file cat data.txt.gz file delete data.txt.gz echo echo ======== echo Test 51 echo ======== echo write filetest1.ped write bin filetest.bin clear echo echo ======== echo Test 52 echo ======== echo read bin filetest.bin write filetest2.ped set ple -2 silent eval (define (same file1 file2) \ (begin \ (define p1 (open-input-file file1)) \ (define p2 (open-input-file file2)) \ (let loop ((lin1 (read-line p1)) \ (n1 1) \ (lin2 (read-line p2)) \ (n2 1)) \ (if (and (string? lin1) (string? lin2)) \ (if (string=? lin1 lin2) \ (loop (read-line p1) \ (+ n1 1) \ (read-line p2) \ (+ n2 1)) \ (begin (display "Different at: ") \ (display (string=? lin1 lin2)) \ (newline) \ (display n1) (display ":") (display lin1) \ (newline) \ (display n2) (display ":") (display lin2) \ (newline))) \ (if (and (equal? lin1 lin2) (not lin1)) \ (begin \ (display "Files ") \ (write file1) \ (display " and ") \ (write file2) \ (display " are the same") \ (newline)) \ (begin (display "One file shorter!") (newline))))) \ (close-input-port p1) \ (close-input-port p2))) set ple -1 eval (same "filetest1.ped" "filetest2.ped") file delete filetest.bin filetest1.ped filetest2.ped clear echo echo Testing reading, writing, deleting files and Scheme scripting: echo echo ======== echo Test 53 echo ======== echo eval (define (ranint n) \ (let loop ((i 1)) \ (if (<= i n) \ (begin \ (display (random 10000000)) (newline) \ (loop (+ i 1))) \ (newline)))) macro ranfam output %% eval (ranint %1) output read cases %% run file delete %% output hash.out hash size 96 output ;;;; set seeds 12345 12345 12345 ranfam 2872 clear ranfam 2872 clear ranfam 2872 clear ranfam 2872 clear ranfam 2872 clear echo echo Testing hashing: echo file cat hash.out out cleanhash.out file print /Hashed/ NR 2 5 hash.out out dec loc 2q read case cleanhash.out run echo echo ======== echo Test 54 echo ======== echo set loc probes qua (probes = (trait1+trait2)/trait1) echo echo ====================================================================== echo Luo and Heileman IEICE Electronic Express 2004\; 1:150-155 found that echo "improved exponential hashing" gave 3.33 probes per key echo for 95\% loaded tables with 3023 buckets filled by random keys echo ====================================================================== echo mean probes echo file delete hash.out cleanhash.out clear # # test the copy command # echo echo Testing the copy command: echo set loc a mar set loc b mar read cases inline 1 x/x C/C 2 A/A x/x 3 A/B x/x 4 B/B x/x 5 x/x x/x ;;;; run echo echo ======== echo Test 55 echo ======== echo copy 3 3 4 4 merge write echo echo ======== echo Test 56 echo ======== echo copy 3 3 4 4 write echo echo ======== echo Test 57 echo ======== echo copy 1 1 2 2 write clear echo echo Testing linear models: echo # # test dataset for regression algorithms from Longley 1967 # Longley, J. W. (1967). # An Appraisal of Least Squares Programs for the # Electronic Computer from the Viewpoint of the User. # Journal of the American Statistical Association, 62, pp. # 819-841. # set loc GNP.deflat qua set loc GNP qua set loc Unemployed qua set loc Armed.Forc qua set loc Population qua set loc Year qua set loc Employed qua read cases inline ! GNP.deflator GNP Unemployed Armed.Forces Population Year Employed 1 83.0 234.289 235.6 159.0 107.608 1947 60.323 2 88.5 259.426 232.5 145.6 108.632 1948 61.122 3 88.2 258.054 368.2 161.6 109.773 1949 60.171 4 89.5 284.599 335.1 165.0 110.929 1950 61.187 5 96.2 328.975 209.9 309.9 112.075 1951 63.221 6 98.1 346.999 193.2 359.4 113.270 1952 63.639 7 99.0 365.385 187.0 354.7 115.094 1953 64.989 8 100.0 363.112 357.8 335.0 116.219 1954 63.761 9 101.2 397.469 290.4 304.8 117.388 1955 66.019 10 104.6 419.180 282.2 285.7 118.734 1956 67.857 11 108.4 442.769 293.6 279.8 120.445 1957 68.169 12 110.8 444.546 468.1 263.7 121.950 1958 66.513 13 112.6 482.704 381.3 255.2 123.366 1959 68.655 14 114.2 502.601 393.1 251.4 125.368 1960 69.564 15 115.7 518.173 480.6 257.2 127.852 1961 69.331 16 116.9 554.894 400.7 282.7 130.081 1962 70.551 ;;;; run echo echo ========================================================== echo The NIST results are: echo Beta Standard Error echo echo Intercept -3482.25863459582 890.420383607373 echo GNP.deflat 0.0150618722713733 0.0849149257747669 echo GNP -0.0358191792925910 0.0334910077722432 echo Unemployed -0.0202022980381683 0.00488399681651699 echo Armed.Forc -0.0103322686717359 0.00214274163161675 echo Population -0.0511041056535807 0.226073200069370 echo Year 1.82915146461355 0.455478499142212 echo echo Model Mean Square 30.6954003240823 echo Mean Square Error 0.0929360061673238 echo R-Squared 0.995479004577296 echo ========================================================== echo echo ======== echo Test 58 echo ======== regress Employed on GNP.deflat GNP Unemployed Armed.Forc Population Year echo echo echo ================================================================================= echo For principal components analysis, R princomp() gives: echo Eigenvectors: echo echo 5.5330676785 1.1875546443 0.2522163113 0.0152385220 echo 0.0106362646 0.0010279413 0.0002586380 echo Eigenvalues: echo -0.4225559 0.03331479 0.04154777 0.68544289 0.5384123 -0.22754105 -0.08435441 echo -0.4232763 0.03003906 0.15667625 -0.18863757 0.2148123 0.50920350 0.67407027 echo -0.2791521 -0.61726052 -0.67738968 0.07297657 -0.2248161 -0.06320698 0.14947835 echo -0.1887305 0.77656258 -0.58598762 -0.04866667 -0.1046508 -0.05290781 0.04278298 echo -0.4218501 -0.06924115 0.08434184 -0.66741256 0.2739382 -0.51075414 -0.16965609 echo -0.4247835 -0.02365912 0.03157581 -0.04933020 -0.1339253 0.57803987 -0.68081026 echo -0.4127227 0.09259423 0.40419980 0.19752696 -0.7137896 -0.29519928 0.14850470 echo echo ================================================================================= echo echo ======== echo Test 59 echo ======== echo pca clear echo echo echo Testing permutation contingency chi-square: echo # # Sparse table from Mehta et al J Classification 1990; 7:111-4 # Exact Pearson X2 P= 0.0013 (StatXact) or 0.0015 (fisher.test) # Sib-pair, by contrast, uses the LRTS (Gibbs X2). # # Second table from Mehta and Patel (1983), and used by i # Newton and Geyer (1994), and Davison and Hinkley (1997) # set iter 1000 chi 3 9 0 7 0 0 0 0 0 1 1 1 1 1 1 1 1 1 0 0 0 8 0 0 0 0 0 0 0 chi 7 5 1 2 2 1 1 0 1 2 0 0 2 3 0 0 0 1 1 1 2 7 3 1 1 2 0 0 0 1 0 1 1 1 1 0 0 set iter 200 clear echo echo echo Testing Kruskal-Wallis test: echo # # Kruskal-Wallis test # set loc treatment qua set loc response qua read cas inline 1 1 2 2 1 3 3 1 3 4 1 3 5 1 3 6 1 0 7 2 1 8 2 3 9 2 1 10 2 2 11 2 2 12 2 3 13 3 3 14 3 1 15 3 2 16 3 1 17 3 3 18 3 3 19 4 1 20 4 0 21 4 0 22 4 0 23 4 0 24 4 -1 ;;;; run echo echo ======== echo Test 60 echo ======== echo recast response cat tab treatment response recast response cat echo echo ======== echo Test 61 echo ======== echo echo ==================================================== echo Rosner B. Fundamentals of Biostatistics 3rd edition echo Example 12.21 H = 11.806 df = 3 P = 0.008078148 echo echo Data from Abelson et al (1983) echo echo ==================================================== kru response treatment echo echo echo Testing survival analysis: echo clear set loc time qua set loc stadium qua set loc event aff read cases inline # id time stadium event 1 28 1 y 2 89 1 y 3 175 1 y 4 195 1 y 5 309 1 y 6 377 1 n 7 393 1 n 8 421 1 n 9 447 1 n 10 462 1 y 11 709 1 n 12 744 1 n 13 770 1 n 14 1106 1 n 15 1206 1 n 16 34 2 y 17 88 2 y 18 137 2 y 19 199 2 y 20 280 2 y 21 291 2 y 22 299 2 n 23 300 2 n 24 309 2 y 25 351 2 y 26 358 2 y 27 369 2 y 28 369 2 y 29 370 2 y 30 375 2 y 31 382 2 y 32 392 2 y 33 429 2 n 34 451 2 y 35 1119 2 n ;;;; run echo echo ======== echo Test 62 echo ======== echo set ple 0 kaplan-meier time event echo echo ======== echo Test 63 echo ======== echo reg time = stadium weibull event echo echo Note that dummy does not exist: kludge to fit intercept only model! echo reg time = dummy weibull event lrt echo echo ======== echo Test 64 echo ======== echo lifetest 0 time event tim cov stadium echo echo ======== echo Test 65 echo ======== echo surv time event stadium echo echo Survival analysis of pedigree data: echo Cai et al. APOE is linked to Alzheimer's disease in a large pedigree. echo Am J Med Genet (Neuropsychiatr Genet) 1997\; 74: 365-69. echo clear set locus AD aff set locus AD50 aff set locus onset qua set locus age qua set locus apoe marker set locus apoc1 marker read pedigree inline 1 101 x x m x x x x x x x x 1 102 x x f x x x x x x x x 1 201 101 102 m y y 57 x 3 4 1 1 1 202 x x f n n x x 3 4 1 1 1 203 101 102 f y y 62 x x x x x 1 204 x x m n n x x x x x x 1 206 x x f n n x x x x x x 1 205 101 102 m y y 65 65 x x x x 1 207 101 102 m n n x x x x x x 1 208 x x f n n x x x x x x 1 209 101 102 m n n x x x x x x 1 210 x x f n n x x x x x x 1 211 x x m n n x x x x x x 1 301 201 202 m n n x x x x x x 1 302 201 202 m n n 74 74 3 3 1 1 1 336 x x f n n x x x x x x 1 304 x x m n n x x x x x x 1 305 201 202 f y y 54 x 4 4 1 1 1 306 201 202 m n n x x x x x x 1 316 205 206 m y y 69 x 3 4 1 1 1 315 x x f n n x x x x x x 1 317 205 206 f n n x x x x x x 1 341 x x m n n x x x x x x 1 318 205 206 f n n x x x x x x 1 337 x x m n n x x x x x x 1 319 205 206 f n n x x x x x x 1 321 x x f n n x x x x x x 1 320 205 206 m y y x x x x x x 1 322 205 206 m n n x x x x x x 1 323 205 206 m n n x x x x x x 1 338 209 210 m n n 73 73 3 3 1 1 1 339 x x f n n x x x x x x 1 340 209 210 m n n 75 75 3 3 1 1 1 342 211 210 f n n 62 62 3 3 1 1 1 343 x x m n n x x x x x x 1 419 302 336 m n n x x x x x x 1 420 302 336 m n n x x x x x x 1 401 x x m n n x x 3 3 1 1 1 402 304 305 f n x 46 46 3 4 1 1 1 403 x x m n n x x x x x x 1 404 304 305 f n x 45 45 3 4 1 1 1 405 304 305 m n x 44 44 3 4 1 1 1 446 316 315 f n x 49 49 3 4 1 2 1 413 316 315 m n n 62 62 3 3 1 1 1 423 316 315 m n n x x x x x x 1 424 316 315 f n x 50 50 2 4 1 2 1 439 341 317 m n n x x x x x x 1 440 341 317 m n n x x x x x x 1 442 341 317 f n n x x x x x x 1 425 337 319 m n n x x x x x x 1 426 320 321 m n n x x x x x x 1 427 320 321 m n n x x x x x x 1 428 320 321 m n n x x x x x x 1 437 338 339 m n n 54 54 3 3 1 1 1 438 338 339 f n n x x x x x x 1 445 343 342 m n x 46 46 3 3 1 1 1 307 x x m n n x x x x x x 1 308 204 203 f n n 65 65 3 4 1 1 1 309 204 203 m y y 64 x 4 4 1 1 1 310 x x f n n x x 3 4 1 1 1 311 204 203 f y y 59 x x x x x 1 312 x x m n n x x 3 4 1 1 1 313 204 203 m n n x x x x x x 1 314 x x f n n x x 2 3 1 1 1 325 207 208 f y y x x x x x x 1 324 x x m n n x x x x x x 1 327 207 208 m y y 65 x x x x x 1 326 x x f n n x x x x x x 1 328 207 208 m y y 60 x x x x x 1 329 x x f n n x x x x x x 1 331 207 208 f x x 74 74 3 3 1 1 1 330 x x m n n x x x x x x 1 333 207 208 f n n x x x x x x 1 334 207 208 m n n x x x x x x 1 335 x x f n n x x x x x x 1 406 307 308 f n x 45 45 3 4 1 1 1 407 307 308 m n x 44 44 3 4 1 1 1 408 309 310 m n x 46 46 3 4 1 1 1 409 312 311 m n x 39 39 3 3 1 1 1 410 312 311 f n x 35 35 3 4 1 1 1 411 313 314 m n n x x x x x x 1 412 313 314 m n n x x x x x x 1 429 324 325 f n n x x x x x x 1 430 324 325 f n n x x x x x x 1 431 324 325 f n n x x x x x x 1 432 324 325 f n n x x x x x x 1 433 327 326 f n n x x x x x x 1 434 327 326 m n n x x x x x x 1 416 328 329 f n n x x x x x x 1 415 x x m n n x x x x x x 1 435 328 329 f n n x x x x x x 1 436 330 331 f n x 46 46 3 3 1 1 1 443 330 331 m n n 58 58 3 3 1 1 1 418 330 331 f n n 60 60 3 3 1 1 1 417 x x m n n x x 3 4 1 1 1 444 334 335 f n x 50 50 3 3 1 1 1 501 415 416 m n x 26 26 2 3 1 1 1 502 415 416 f n x 27 27 3 3 1 1 1 503 417 418 m n x 35 35 3 3 1 1 1 504 403 404 m n n x x x x x x ;;;; run echo echo ======== echo Test 66 echo ======== echo surv onset AD echo echo Testing categorical trait gene-dropping association: echo clear set loc a qua set loc b mar read cases inline 1 1 1/1 2 2 x/x 3 1 1/2 4 3 1/2 5 3 1/2 6 1 1/1 7 1 1/1 8 1 1/1 9 1 1/1 ;;;; run echo echo ======== echo Test 67 echo ======== echo set ple 1 ass a cat set ple -1 clear echo echo Testing handling of twins: echo set locus zyg qua set locus mar marker set locus qtrait qua set twin zyg merlin read pedigree inline 1 1 x x m x 1/1 10 1 2 x x f x 1/2 20 1 3 1 2 m 1 1/1 11 1 4 1 2 m 1 1/2 10 1 5 x x f x 1/2 19 1 6 x x f x 1/2 22 1 7 3 5 f x 1/1 11 1 8 4 6 f 2 1/1 9 1 9 4 6 m 2 1/2 18 2 3 1 2 m 1 1/1 11 2 4 1 2 m 1 x/x x 2 5 4 6 m x 2/2 8 ;;;; set error_drop on run echo echo ======== echo Test 68 echo ======== echo wri echo echo ======== echo Test 69 echo ======== echo kinship echo echo ======== echo Test 70 echo ======== echo var qtrait echo echo ======== echo Test 71 echo ======== echo var qtrait cov mar clear echo echo Testing sex: echo set locus AMELXY marker set locus xmarker xmarker read pedigree inline 1 1 x x m C/G 1/2 1 2 x x f C/G 3/4 1 3 x x m C/C 5/5 1 4 x x f C/C 6/6 ;;;; set che off run set sex marker AMELXY test sex clear echo echo Testing various genetic analyses: echo echo echo Pedigrees from the online supplementary data echo (http://www.gene.ucl.ac.uk/anhumgen/web2.doc) for echo Cavanaugh JA et al (1998). echo Analysis of Australian Crohn's disease pedigrees refines the localisation for echo susceptibility to inflammatory bowel disease on chromosome 16. echo Ann Hum Genet 62: 291-298. echo set seeds 4576 123 2354 set loc ibd aff . set loc D16S769 mar 53.713 26066263 (chr 16) set loc D16S3145 mar 55.012 26784604 (chr 16) set loc D16S753 mar 60.125 31181005 (chr 16) set loc D16S409 mar 60.998 47333369 (chr 16) set loc D16S411 mar 62.226 48294236 (chr 16) # CARD15 49139742-49399041 set loc D16S419 mar 67.694 51510863 (chr 16) set loc D16S415 mar 69.148 52228236 (chr 16) set loc D16S771 mar 70.852 53066505 (chr 16) read pedigree inline #--- Page 1 a-i ---- 1a 1 x x m n 3/4 3/4 3/5 1/3 3/5 4/5 7/8 x/x 1a 2 x x f n 4/5 4/8 4/5 1/6 4/7 3/5 4/8 x/x 1a 3 1 2 f y 4/4 4/4 4/5 3/6 3/4 4/5 4/7 1/4 1a 4 1 2 f y 4/5 4/4 4/5 3/6 3/4 4/5 4/7 1/4 1b 1 x x m n 1/4 2/4 3/4 3/6 2/3 1/7 4/9 x/x 1b 2 x x f n 4/4 2/2 1/5 3/3 4/5 5/5 2/4 1/3 1b 3 1 2 f y 1/4 2/2 1/3 3/6 2/4 5/7 2/4 3/5 1b 4 1 2 f y 1/4 2/2 1/3 3/6 2/5 5/7 2/4 3/5 1c 1 x x m n x/x 2/4 3/6 x/x x/x x/x x/x x/x 1c 2 x x f n 2/5 4/5 4/6 3/6 2/4 5/7 4/8 3/4 1c 3 1 2 f y 3/5 4/4 6/6 2/3 4/4 1/5 4/8 3/4 1c 4 1 2 f y 3/5 2/4 3/6 2/3 4/4 1/5 4/8 3/4 1d 1 x x m n 4/4 4/4 3/5 3/6 2/3 5/7 3/7 1/4 1d 2 x x f n 4/5 4/6 3/5 3/8 2/3 1/5 3/8 4/5 1d 3 1 2 f y 4/4 4/6 3/3 3/6 3/3 1/7 3/8 4/4 1d 4 1 2 f y 4/4 4/6 3/3 3/6 3/3 1/7 3/7 4/5 1e 1 x x m n 3/5 x/x x/x x/x 3/4 x/x 3/8 x/x 1e 2 x x f n 3/4 4/5 4/5 3/4 3/4 3/5 3/6 3/4 1e 3 1 2 f y 3/4 4/5 4/6 3/3 3/3 3/5 3/8 3/5 1e 4 1 2 f y 3/3 4/4 5/6 3/4 3/3 3/5 3/8 3/5 1e 5 1 2 f y 3/5 4/4 4/5 3/4 3/4 5/5 3/6 4/5 1f 1 x x m n 3/4 4/7 4/4 3/3 1/3 5/6 8/10 3/4 1f 2 x x f y 3/4 2/4 2/6 2/3 4/5 1/5 3/4 5/7 1f 3 1 2 f y 3/3 4/4 2/4 2/3 3/4 5/5 3/8 3/7 1f 4 1 2 f y 3/4 2/4 4/6 2/3 3/4 5/5 3/8 4/7 1g 1 x x m n 2/4 4/4 2/6 2/3 1/5 3/6 3/8 3/7 1g 2 x x f n 4/5 2/4 1/5 1/3 3/6 1/5 7/8 2/5 1g 3 1 2 f y 4/5 2/4 5/6 1/3 1/3 3/5 3/8 2/3 1g 4 1 2 f y 2/4 4/4 1/2 2/3 5/6 1/6 7/8 2/3 1h 1 x x m n 3/5 4/4 3/3 2/3 2/6 5/6 8/8 3/6 1h 2 x x f n 2/5 4/5 3/3 3/4 2/3 1/5 1/3 3/3 1h 3 1 2 f y 2/5 4/4 3/3 2/3 2/6 1/5 1/8 x/x 1h 4 1 2 f y 3/5 4/5 3/3 3/4 2/3 1/6 3/8 x/x 1i 1 x x m n 4/4 4/4 3/6 2/3 4/5 5/6 7/8 2/4 1i 2 x x f n 2/3 4/6 4/6 1/2 1/5 5/6 7/8 3/3 1i 3 1 2 f y 3/4 4/6 4/6 1/2 1/5 5/5 7/8 3/4 1i 4 1 2 f y 3/4 4/6 4/6 1/2 1/5 5/5 7/8 3/4 #--- Page 2 a-i ---- 2a 1 x x m n 2/5 4/7 2/6 1/3 3/4 4/5 2/4 3/4 2a 2 x x f n 5/5 4/4 4/7 3/5 4/5 3/6 3/4 2/5 2a 3 1 2 m y 2/5 4/7 4/6 3/3 4/4 3/4 3/4 3/5 2a 4 1 2 m y 2/5 4/7 6/7 3/5 4/5 3/4 4/4 4/5 2a 5 1 2 f y 5/5 4/4 2/4 1/3 3/4 5/6 2/3 2/3 2b 1 x x m n 3/4 4/7 4/6 1/3 3/4 5/8 1/8 x/x 2b 2 x x f n x/x 1/4 4/6 3/6 4/5 3/5 3/12 x/x 2b 3 1 2 f y 3/4 4/7 4/6 3/3 4/4 3/5 3/8 4/7 2b 4 1 2 m y 3/4 4/7 4/6 3/3 4/4 5/5 3/8 4/4 2c 1 x x m n 2/4 2/4 4/5 3/7 2/3 1/5 7/8 3/5 2c 2 x x f n 3/5 3/4 2/4 1/3 3/5 5/5 3/7 3/3 2c 3 1 2 f y 4/5 4/4 2/5 3/3 3/3 1/5 3/7 3/3 2c 4 1 2 f y 4/5 4/4 2/5 3/3 3/3 1/5 3/7 3/3 2d 1 x x m n 4/5 4/5 5/6 1/6 4/5 1/1 4/10 5/5 2d 2 x x f n x/x 4/9 x/x x/x 2/5 5/6 1/3 3/4 2d 3 1 2 m y 4/4 4/9 4/5 1/3 2/5 1/6 1/10 4/5 2d 4 1 2 m y 4/4 4/9 4/5 1/3 2/5 1/6 1/10 3/5 2e 1 x x m n 4/5 4/5 3/3 3/7 2/3 3/6 3/8 3/4 2e 2 x x f n 5/5 5/5 3/6 3/6 3/5 4/5 4/6 2/2 2e 3 1 2 f y 4/5 x/x 3/6 3/6 2/3 3/5 6/8 2/3 2e 4 1 2 f y 5/5 4/5 3/6 6/7 3/3 5/6 3/6 2/4 2f 1 x x m n x/x x/x x/x x/x x/x 4/6 x/x 4/5 2f 2 x x f n 4/5 2/5 10/10 1/5 3/5 1/5 1/8 5/6 2f 3 1 2 m y 4/6 2/4 6/10 1/6 2/3 4/5 1/3 5/6 2f 4 1 2 f y 5/6 4/5 6/10 5/6 3/5 1/6 3/8 4/6 2g 1 x x m n 5/6 4/4 3/6 1/3 4/5 2/5 8/9 3/6 2g 2 x x f n 5/6 3/4 3/4 2/3 3/4 5/7 7/8 4/6 2g 3 1 2 m y 5/5 4/4 4/6 2/3 3/4 5/7 7/8 3/6 2g 4 1 2 m y 5/5 4/4 4/6 2/3 3/4 5/7 7/8 3/6 2h 1 x x m n x/x 4/7 x/x x/x x/x 1/6 x/x 1/2 2h 2 x x f n 4/6 4/6 2/5 3/6 1/7 1/4 3/7 3/5 2h 3 1 2 m y 5/6 4/4 2/5 1/6 4/7 4/6 3/4 2/3 2h 4 1 2 f y 5/6 4/4 2/5 1/6 4/7 4/6 3/4 2/3 2h 5 1 2 m y 5/6 4/7 2/5 1/6 1/7 1/4 3/4 1/3 2i 1 x x m n 4/8 2/4 2/5 2/3 3/5 4/6 4/8 2/3 2i 2 x x f n 4/5 3/4 4/5 6/7 2/5 4/5 8/9 3/4 2i 3 1 2 f y 4/8 3/4 2/5 3/6 2/3 4/6 4/9 3/4 2i 4 1 2 f y 5/8 4/4 4/5 3/7 2/3 4/4 8/9 3/4 #--- Page 3 a-i ---- 3a 1 x x m n x/x 4/5 5/7 1/3 3/7 x/x 7/8 1/5 3a 2 x x f n 4/5 2/5 3/4 6/7 5/7 4/4 3/8 4/6 3a 3 1 2 f y 4/4 2/4 4/7 3/7 3/5 1/4 7/8 1/6 3a 4 1 2 m y 4/5 2/4 4/7 3/7 3/7 1/4 7/8 4/5 3b 1 x x m n x/x x/x x/x x/x x/x x/x x/x x/x 3b 2 x x f n x/x x/x x/x x/x x/x x/x x/x x/x 3b 6 x x f n 4/5 2/4 4/7 3/5 4/5 4/7 3/4 3/4 3b 3 1 2 m n 5/5 4/7 4/6 1/3 4/5 1/4 3/3 3/4 3b 4 1 2 m y 5/5 2/4 4/5 2/7 3/5 2/5 3/4 3/4 3b 5 1 2 m y 5/5 4/7 4/5 2/7 3/5 2/5 3/4 3/4 3b 7 5 6 m y 5/5 4/4 5/7 2/3 5/5 4/5 3/4 3/4 3b 8 5 6 f y 5/5 2/4 5/7 2/3 5/5 4/5 3/4 3/4 3c 1 x x m n 2/4 2/4 4/5 3/7 4/5 1/2 3/9 4/4 3c 2 x x f n 4/5 4/5 1/4 2/3 1/6 2/3 1/9 3/7 3c 3 1 2 f y 4/4 4/4 4/5 2/3 5/6 2/2 1/9 3/4 3c 4 1 2 f y 4/4 4/4 4/5 2/3 5/6 1/2 1/3 3/4 3d 1 x x m n x/x x/x 4/6 x/x x/x 1/3 1/7 3/4 3d 2 x x f n 2/5 4/5 3/4 3/3 3/5 4/6 7/8 4/4 3d 3 1 2 f y 4/5 4/5 4/6 3/3 3/3 3/6 1/8 4/4 3d 4 1 2 m y 4/5 5/5 4/4 3/3 3/3 1/6 7/8 3/4 3d 5 1 2 f y 4/5 5/5 4/4 3/3 3/3 1/6 7/8 3/4 3e 1 x x m n 2/6 4/4 5/5 1/3 2/5 1/6 1/11 5/10 3e 2 x x f n 4/5 2/4 3/4 3/6 3/5 1/5 3/3 1/1 3e 3 1 2 f y 2/4 4/4 4/5 1/6 5/5 1/1 1/3 1/5 3e 4 1 2 f y x/x 2/4 4/5 1/6 5/5 1/1 1/3 1/5 3f 1 x x m n x/x 4/6 5/6 2/6 2/4 5/7 3/4 x/x 3f 2 x x f y 3/4 2/4 5/6 2/4 3/5 5/6 7/13 2/4 3f 3 1 2 m y 4/5 4/4 6/6 4/6 4/5 5/6 4/7 2/4 3f 4 1 2 m y 3/4 2/4 5/5 2/2 2/3 5/7 3/13 3/4 3g 1 x x m n 4/5 4/7 6/6 3/3 1/2 3/6 3/7 4/4 3g 2 x x f n 3/3 4/5 4/6 1/3 2/3 1/4 3/5 3/4 3g 3 1 2 m y 3/5 4/4 4/6 1/3 1/3 3/4 3/5 3/4 3g 4 1 2 m y 3/5 4/5 4/6 1/3 1/2 1/3 3/3 4/4 3h 1 x x m n 4/4 2/4 3/4 1/3 3/5 1/5 4/8 4/7 3h 2 x x f n 5/6 x/x 1/9 1/2 3/6 1/6 x/x 4/5 3h 3 1 2 m y 4/6 2/7 3/9 1/3 3/3 1/1 3/8 4/4 3h 4 1 2 m y 4/5 2/4 1/3 2/3 3/6 1/6 3/8 4/5 3i 1 x x m n 3/5 4/7 5/6 1/3 4/5 1/1 x/x 4/5 3i 2 x x f n 5/6 4/7 2/3 1/3 4/4 4/5 x/x 3/5 3i 3 1 2 f y 5/6 4/7 2/6 1/3 4/4 1/4 x/x 4/5 3i 4 1 2 f y 5/6 4/4 2/5 1/1 x/x 1/5 x/x 3/4 #--- Page 4 a-i ---- 4a 1 x x m n 4/4 4/4 3/6 3/6 3/4 5/5 3/8 3/5 4a 2 x x f n 5/5 2/4 5/6 2/3 2/4 1/5 3/4 4/5 4a 3 1 2 m y 4/5 4/4 5/6 2/6 2/4 1/5 3/4 3/4 4a 4 1 2 f y 4/5 4/4 5/6 2/6 2/4 5/5 3/8 5/5 4b 1 x x m n 5/6 4/7 4/5 1/3 3/5 x/x 1/3 1/2 4b 2 x x f n 4/4 1/7 6/6 3/3 3/3 3/5 8/9 2/3 4b 3 1 2 f y 4/6 7/7 4/6 3/3 3/5 3/5 1/9 2/3 4b 4 1 2 f y 4/5 1/4 5/6 1/3 3/3 1/3 3/9 2/2 4c 1 x x m n 4/5 4/7 2/7 3/7 2/3 3/6 2/3 3/4 4c 2 x x f n 3/5 2/7 5/5 1/3 5/6 6/7 3/8 3/5 4c 3 1 2 f y 3/4 4/7 2/5 1/3 2/6 6/6 2/3 3/4 4c 4 1 2 f y 3/5 7/7 5/7 3/3 3/5 3/7 3/8 3/4 4c 5 1 2 f y 3/5 7/7 5/7 3/3 3/5 3/6 2/3 3/4 4d 1 x x m n 4/5 4/4 2/4 1/6 1/3 4/8 x/x 3/4 4d 2 x x f n 4/5 2/5 4/4 3/6 3/5 4/7 3/4 3/5 4d 3 1 2 m y 4/5 2/4 4/4 3/6 1/3 4/8 4/8 3/3 4d 4 1 2 f y 5/5 4/5 4/4 3/6 1/3 7/8 3/8 3/5 4d 5 1 2 m y 4/5 2/4 4/4 3/6 3/3 4/4 4/8 3/4 4e 1 x x m n x/x x/x 3/6 6/7 2/5 5/7 x/x 3/4 4e 2 x x f n 5/6 5/7 4/4 7/9 4/7 5/6 3/4 4/6 4e 3 1 2 m y 5/6 4/5 4/6 7/9 4/5 5/7 3/8 4/4 4e 4 1 2 m y 4/6 4/7 4/6 7/7 2/4 6/7 3/8 4/6 4f 1 x x m n 5/6 2/4 4/6 3/3 2/4 6/6 4/4 3/5 4f 2 x x f n 4/4 4/4 3/4 5/6 4/5 1/1 6/15 4/6 4f 3 1 2 m y 4/5 2/4 3/4 3/6 4/4 1/6 4/15 3/4 4f 4 1 2 m y 4/5 2/4 4/4 3/5 4/5 1/6 4/6 4/5 4g 1 x x m n x/x 4/7 3/7 3/6 x/x 1/5 4/8 5/6 4g 2 x x f n 5/5 4/5 2/4 3/3 4/5 1/7 3/8 3/4 4g 3 1 2 m y 5/5 5/7 2/3 3/6 4/6 1/1 3/8 4/5 4g 4 1 2 f y 5/5 4/4 3/4 3/3 5/6 1/1 3/8 4/5 4h 1 x x m n 4/5 4/7 4/6 2/3 2/3 3/4 3/9 3/5 4h 2 x x f n 4/6 2/4 5/5 3/3 2/3 3/5 7/8 3/6 4h 3 1 2 f y 4/6 2/7 5/6 2/3 2/3 3/5 3/8 3/6 4h 4 1 2 m y 4/6 2/4 4/5 3/3 2/2 4/5 8/9 3/5 4i 1 x x m n x/x x/x 3/7 x/x x/x x/x x/x 5/6 4i 2 x x f n 4/5 4/7 3/6 3/3 3/4 5/6 3/8 4/4 4i 3 1 2 f y 4/6 4/5 3/3 3/3 2/4 5/6 3/8 4/6 4i 4 1 2 m y 4/6 4/5 3/3 3/3 2/4 5/6 3/8 4/5 4i 5 1 2 m y 4/6 4/5 3/7 3/3 2/4 6/6 3/8 4/6 #--- Page 5 a-i ---- 5a 1 x x m n 4/5 4/7 4/6 3/10 4/5 5/6 1/8 2/5 5a 2 x x f n 3/4 2/7 2/5 3/7 3/4 5/8 3/3 4/5 5a 3 1 2 f y 3/4 2/4 2/6 3/3 3/5 6/8 3/8 2/4 5a 4 1 2 m y 4/4 4/7 5/6 3/7 4/5 5/6 3/8 2/5 5b 1 x x m n 4/6 x/x 4/6 x/x x/x x/x 8/9 3/4 5b 2 x x f n 3/4 4/4 3/6 1/7 4/4 6/7 3/8 5/7 5b 3 1 2 f y 4/4 4/4 3/4 1/3 3/4 5/6 8/8 4/7 5b 4 1 2 f y 4/4 4/4 3/6 1/3 3/4 5/6 8/8 4/7 5c 1 x x m n 5/5 4/4 1/3 2/3 1/5 5/6 3/8 4/4 5c 2 x x f n 4/6 4/7 2/4 3/3 2/5 5/5 7/8 6/6 5c 3 1 2 m y 4/5 4/7 3/4 2/3 1/5 5/5 3/8 4/6 5c 4 1 2 m y 4/5 4/7 3/4 2/3 1/5 5/5 3/8 4/6 5d 1 x x m n x/x x/x x/x x/x x/x 4/6 x/x x/x 5d 2 x x f n 4/5 2/4 4/5 2/3 3/4 4/6 x/x 4/4 5d 3 1 2 f y 5/5 2/4 3/4 3/3 3/3 4/6 3/4 4/4 5d 4 1 2 f y 5/5 2/4 3/4 3/3 3/3 6/6 1/4 4/4 5e 1 x x m n 4/5 2/7 2/7 3/3 3/5 1/5 7/9 4/6 5e 2 x x f n 4/6 2/4 3/4 x/x 3/5 4/5 8/8 4/4 5e 3 1 2 m y 4/5 4/7 2/4 3/3 3/3 1/4 8/9 4/6 5e 4 1 2 f y 4/5 4/7 2/4 3/3 3/3 1/4 8/9 4/6 5f 1 x x m n 4/5 2/4 4/6 1/3 4/6 1/6 3/4 3/5 5f 2 x x f n x/x 2/6 1/5 1/6 3/7 1/2 7/8 3/5 5f 3 1 2 f y 4/4 2/2 4/5 3/6 6/7 1/2 3/8 3/5 5f 4 1 2 m y 4/4 2/2 5/6 1/6 3/4 1/6 4/7 3/5 5g 1 x x m n 3/5 4/4 4/6 3/7 2/6 3/5 3/15 2/3 5g 2 x x f n 3/6 4/4 3/4 3/3 3/6 1/3 8/9 2/3 5g 3 1 2 f y 3/3 4/4 4/4 3/3 3/6 1/5 3/8 2/3 5g 4 1 2 f y 5/6 4/4 4/4 3/7 2/3 1/3 3/8 3/3 5h 1 x x m n 3/5 4/4 4/6 3/7 2/6 3/5 3/15 2/3 5h 2 x x f n 3/6 4/4 3/4 3/3 3/6 1/3 8/9 2/3 5h 3 1 2 f y 3/3 4/4 4/4 3/3 3/6 1/5 3/8 2/3 5h 4 1 2 f y 5/6 4/4 4/4 3/7 2/3 1/3 3/8 3/3 5i 1 x x m n 2/2 4/5 2/4 2/3 3/5 5/6 7/8 3/5 5i 2 x x f n 3/5 4/5 4/6 2/3 3/3 2/5 7/9 3/4 5i 3 1 2 f y 2/5 5/5 4/6 2/3 3/3 5/5 7/8 3/4 5i 4 1 2 f y 2/3 4/4 4/6 2/3 3/5 2/5 8/9 3/3 #--- Page 6 a-i ---- 6a 1 x x m n 4/5 4/6 4/5 1/3 1/2 4/4 4/8 2/5 6a 2 x x f n 1/5 4/6 1/2 2/3 1/2 4/4 4/8 3/5 6a 3 1 2 f y x/x 4/6 2/5 1/3 1/2 4/4 8/8 5/5 6a 4 1 2 f y 4/5 4/4 1/5 1/3 1/2 4/4 8/8 5/5 6b 1 x x m n x/x x/x x/x x/x x/x 5/6 x/x x/x 6b 2 x x f n 3/4 4/7 4/5 1/3 4/6 2/5 4/9 3/6 6b 3 1 2 f y 3/5 4/7 4/5 1/2 2/4 5/5 8/9 3/6 6b 4 1 2 f y 3/5 4/7 4/5 1/2 2/4 5/6 8/9 3/6 6c 1 x x m n 2/5 4/4 6/6 3/6 2/4 5/5 8/8 4/4 6c 2 x x f n 3/5 4/5 3/4 3/7 4/5 x/x 3/8 x/x 6c 3 1 2 f y 5/5 4/4 4/6 6/7 4/4 1/5 3/8 3/4 6c 4 1 2 f y 3/5 4/5 4/6 3/6 4/4 1/5 8/8 3/4 6d 1 x x m n 2/6 4/5 6/7 3/5 3/5 4/5 5/8 3/4 6d 2 x x f n 3/5 4/6 3/7 2/2 3/5 4/4 3/8 1/5 6d 3 1 2 f y 5/6 4/6 3/6 2/3 5/5 4/4 5/8 1/4 6d 4 1 2 f y 3/6 4/4 6/7 2/3 5/5 4/4 5/8 1/4 6e 1 x x m n 3/5 1/2 3/6 1/1 6/8 x/x 3/8 2/4 6e 2 x x f y 3/5 2/2 3/3 1/3 2/6 x/x 8/8 4/4 6e 3 1 2 m y x/x 2/2 3/3 1/1 2/6 5/6 x/x 2/4 6e 4 1 2 m y 5/5 2/2 3/6 1/1 2/6 6/7 3/8 2/4 6f 1 x x m n x/x x/x x/x x/x x/x 4/6 3/8 3/5 6f 2 x x f n 3/3 1/4 6/6 3/3 2/6 1/4 3/7 4/4 6f 3 1 2 f y 3/3 4/4 6/6 3/3 2/5 4/4 3/8 4/5 6f 4 1 2 f y x/x 1/4 6/6 3/3 5/6 1/6 3/3 4/5 6g 1 x x m n x/x x/x x/x x/x x/x x/x x/x x/x 6g 2 x x f n x/x 5/8 4/6 x/x 4/7 1/2 x/x x/x 6g 3 1 2 f y x/x 5/7 3/6 1/1 4/7 1/8 1/1 1/1 6g 4 1 2 f y x/x 7/8 3/6 1/1 4/7 1/8 1/1 1/1 6h 1 x x m y 5/5 4/4 2/6 3/3 7/7 1/5 3/7 2/5 6h 2 x x f n 2/3 2/5 4/6 3/6 7/7 1/5 3/8 4/5 6h 3 1 2 f y 3/5 2/4 6/6 3/3 7/7 1/5 7/8 2/5 6h 4 1 2 f y 2/5 4/5 2/4 3/6 7/7 5/5 3/7 4/5 6h 5 1 2 m y 2/5 4/5 4/6 3/6 7/7 5/5 3/7 2/4 6i 1 x x m n x/x x/x x/x x/x x/x x/x x/x x/x 6i 2 x x f n x/x x/x x/x x/x x/x x/x x/x x/x 6i 3 x x m n 4/5 4/7 5/5 6/6 3/3 1/6 2/3 4/5 6i 4 1 2 f y 3/4 4/4 4/5 3/3 3/3 5/6 4/8 4/5 6i 5 1 2 f y 3/4 4/4 4/4 3/3 3/3 5/6 4/7 4/5 6i 6 3 4 f y 3/5 4/4 4/5 3/6 3/3 6/6 2/4 4/5 6i 7 3 4 f y 4/5 4/4 4/5 3/6 3/3 6/6 2/4 4/4 ;;;; run echo echo ======== echo Test 72 echo ======== echo describe ibd echo echo ======== echo Test 73 echo ======== echo show loci echo echo ======== echo Test 74 echo ======== echo drop where hwe undrop echo echo echo ======== echo Test 75 echo ======== echo keep where hwe < 0.01 undrop echo echo ======== echo Test 76 echo ======== echo drop whe num >= 92 undrop echo echo ======== echo Test 77 echo ======== echo drop whe num 0.4 undrop echo echo ======== echo Test 78 echo ======== echo drop whe num >= 92 undrop echo echo ======== echo Test 79 echo ======== echo keep where position 54 63 undrop echo echo ======== echo Test 80 echo ======== echo describe snp echo echo ======== echo Test 81 echo ======== echo linkage echo echo ======== echo Test 82 echo ======== echo show map echo echo ======== echo Test 83 echo ======== echo show ids echo echo ======== echo Test 84 echo ======== echo set iterations 50 echo echo ======== echo Test 85 echo ======== echo apm ibd echo echo ======== echo Test 86 echo ======== echo apm ibd ibd echo echo ======== echo Test 87 echo ======== echo tdt ibd clear echo echo Family 26 from hypercholesterolemia study of Williams et al JAMA 1986 echo used to establish linkage to LDL-R RFLP in Leppert et al echo Am J Hum Genet 1986\; 39: 300-6 and reanalysed by several authors echo eg Guo & Thompson AJHG 1992; 51:1111-26 echo set seeds 4576 123 2354 set locus age qua set locus CHD aff set locus carrier aff set locus adjChol qua set locus ldl mar read pedigree inline 26 101 x x m 62 y y x x x 26 102 x x f 91 y n x x x 26 201 101 102 m 47 y y x x x 26 202 x x f x n n x x x 26 203 101 102 f 71 n y 227 2 2 26 204 x x m x x n x x x 26 301 201 202 f x x n x x x 26 302 201 202 m 38 y y x x x 26 303 x x f 53 n n 92 2 2 26 304 201 202 m x x y 243 1 2 26 305 x x f x x n 93 1 1 26 306 201 202 m x x y 239 1 2 26 307 201 202 m 46 y y 207 1 2 26 308 x x f 42 n n 145 1 1 26 309 201 202 f x x n 21 1 1 26 310 201 202 m x x y x x x 26 311 x x f 47 n n 98 1 2 26 312 201 202 m x y y x x x 26 313 x x f x x n 115 1 1 26 314 201 202 m x x n 92 1 1 26 315 x x f x x n x x x 26 316 204 203 m 45 y y x x x 26 317 204 203 m 32 y y x x x 26 318 x x f 47 n n 134 1 1 26 319 204 203 f x x n 104 1 2 26 320 204 203 f x x n 99 1 2 26 401 302 303 f 31 n n 168 1 2 26 402 302 303 f 29 n y 301 2 2 26 403 x x m x x n 69 1 1 26 404 302 303 f 27 n n 154 1 2 26 405 x x m x x n 143 1 1 26 406 304 305 f 20 n n 68 1 1 26 407 304 305 m 18 n n 56 1 1 26 408 304 305 f 16 n y 316 1 2 26 409 307 308 m 22 n n 194 1 1 26 410 307 308 f 21 n y 417 1 2 26 411 307 308 m 19 n n 205 1 1 26 412 307 308 m 18 n y 284 1 2 26 413 307 308 f 17 n n 115 1 1 26 414 307 308 f 12 n n 210 1 1 26 415 310 311 f 19 n n 105 1 1 26 416 310 311 f 16 n n 126 1 1 26 417 x x m x x n 112 1 1 26 418 312 313 f 15 n y 372 1 2 26 419 312 313 f 14 n n 101 1 1 26 420 312 313 m 13 n y 349 1 2 26 421 312 313 m 6 n y 253 1 2 26 422 316 315 f 24 n y 479 1 2 26 423 317 318 f 22 n n 140 1 1 26 424 x x m x x n x x x 26 425 317 318 f 29 n y 553 1 2 26 426 x x m x x n x x x 26 501 403 402 m x x y 375 1 2 26 502 403 402 m x x n 147 1 2 26 503 403 402 f x x y 299 1 2 26 504 405 404 m x x n 57 1 1 26 505 405 404 m x x n 82 1 1 26 506 417 418 f x x n 125 1 1 26 507 424 425 f x x n 136 1 1 26 508 426 425 m x x n 183 1 1 ;;;; run echo echo ======== echo Test 88 echo ======== echo typ echo echo ======== echo Test 89 echo ======== echo typ CHD echo echo ======== echo Test 90 echo ======== echo tab echo echo ======== echo Test 91 echo ======== echo tab CHD carrier echo echo ======== echo Test 92 echo ======== echo tab CHD ldl set loc logChol qua echo echo ======== echo Test 93 echo ======== echo logChol = log(adjChol) echo echo ======== echo Test 94 echo ======== echo echo ================================================================= echo SAGE (6.0.1) FCOR gives: echo Count Correlation EqvCnt StdError P-values echo echo ----------------------------------------------------------------- echo Marital 5 -0.8588561 5.6 0.237164 0.037602 * echo Grandparental 11 0.4845441 19.6 [0.185177] 0.031421 * echo Avuncular 107 -0.0679835 50.6 [0.141430] 0.638674 echo Cousin 143 -0.0399115 90.1 0.105774 0.707001 echo Par-Off 45 -0.0551662 54.8 [0.135952] 0.691061 echo Sibling 44 0.0338719 28.0 0.192224 0.861506 echo echo ================================================================= echo describe logChol echo echo echo ======== echo Test 95 echo ======== echo regress logChol on age CHD ldl echo echo ======== echo Test 96 echo ======== echo mix logChol 2 poo set iter 50 echo echo ======== echo Test 97 echo ======== echo sibpair logChol echo echo ======== echo Test 98 echo ======== echo assoc logChol echo echo ======== echo Test 99 echo ======== echo mgt logChol echo echo ======== echo Test 100 echo ======== echo apm adjChol over 5 ibd echo echo ======== echo Test 101 echo ======== echo apm adjChol over 5 echo echo ======== echo Test 102 echo ======== echo tdt adjChol over 5 echo echo ======== echo Test 103 echo ======== echo tdt logChol echo echo ======== echo Test 104 echo ======== echo ass adjChol over 5 echo echo ======== echo Test 105 echo ======== echo echo echo SUPERLINK 1.6 gives: echo Theta lod echo 0.0001 8.561008 echo 0.01 8.422634 echo 0.025 8.210869 echo 0.05 7.850694 echo 0.075 7.485948 echo 0.1 7.111979 echo 0.2 5.530992 echo 0.3 3.790529 echo 0.4 1.865282 echo set loc trait marker if (carrier) then trait="1/2" if (not carrier) then trait="1/1" lod trait ldl clear echo echo Finnish families containing probands suffering from neuronal ceroid echo lipofuscinosis described in Savukoski et al AJHG 1994\; 55: 695-701. echo Linkage disequilibrium mapping using 3 chromosome 13 loci echo echo D13S162 D13S160 D13S170 echo echo 13q22-31 D13S162 -- 3cM -- D13S160 -- 3 cM -- D13S170 13q31-32 echo echo Numbering of individuals runs as per Figure 1 generation by generation echo and left to right echo set seeds 4576 123 2354 set locus lincl aff set locus oneperfam aff set locus D13S162 nam set locus D13S160 nam set locus D13S170 nam read pedigree inline 1 1 x x m n n 2 4 1 5 5 9 1 2 x x f n n 4 5 3 5 5 7 1 3 1 2 f y y 4 4 5 5 5 5 1 4 1 2 m y n 4 4 5 5 5 5 1 5 1 2 f n n 4 5 3 5 5 7 1 6 1 2 f n n 2 4 1 3 7 9 1 7 1 2 f n n 2 4 1 3 7 9 2 1 x x m n n 4 8 2 5 3 5 2 2 x x f n n 4 6 4 5 1 5 2 3 1 2 m n n 6 8 2 4 1 3 2 4 1 2 m n n 4 6 4 5 5 5 2 5 1 2 f n n 6 8 2 4 1 3 2 6 1 2 m n n 4 8 2 5 3 5 2 7 1 2 m y y 4 4 5 5 5 5 2 8 1 2 m y n 4 4 5 5 5 5 2 9 1 2 f n n 4 8 2 5 3 5 3 1 x x m n n x x x x x x 3 2 x x f n n x x x x x x 3 3 x x f n n 4 7 4 5 5 8 3 4 1 2 m n n 4 7 4 5 5 6 3 5 1 2 m n n 4 7 4 5 5 8 3 6 x x f n n 3 4 4 5 5 7 3 7 4 3 f n n 4 7 4 4 6 8 3 8 4 3 f n n 4 7 4 4 6 8 3 9 4 3 m y y 4 4 4 5 5 6 3 10 5 6 m n n 4 7 4 5 5 8 3 11 5 6 m y n 4 4 5 5 5 5 4 1 x x m n n 4 8 3 5 5 8 4 2 x x f n n 1 4 1 5 2 4 4 3 1 2 m y y 4 4 5 5 2 5 4 4 1 2 m n n 4 8 3 5 2 8 5 1 x x m n n 4 5 1 5 6 10 5 2 x x f n n 4 5 1 6 4 10 5 3 1 2 f n n 4 4 1 1 10 10 5 4 1 2 m n n 4 5 5 6 4 6 5 5 1 2 f n n 4 4 1 5 6 10 6 1 x x m n n 4 5 1 4 3 11 6 2 x x f n n 4 4 2 5 3 10 6 3 1 2 m y y 4 4 1 5 3 3 6 4 1 2 m n n 4 4 1 2 3 10 7 1 x x m n n 3 4 5 6 3 7 7 2 x x f n n 4 6 2 5 4 7 7 3 1 2 f n n 4 4 5 5 7 7 7 4 1 2 f n n 4 6 2 5 4 7 8 1 x x m n n x x x x x x 8 2 x x f n n 2 4 3 5 2 5 8 3 1 2 f n n 2 4 3 5 2 5 8 4 1 2 f y y 4 4 5 5 5 5 8 5 1 2 m n n 1 4 1 5 5 8 9 1 x x m n n 1 4 1 5 2 5 9 2 x x f n n 4 7 2 5 5 5 9 3 1 2 m n n 1 7 1 5 5 5 9 4 1 2 f y y 4 7 5 5 2 5 10 1 x x m n n 2 5 4 5 5 7 10 2 x x f n n 4 7 2 5 5 7 10 3 1 2 f n n 4 5 4 5 5 7 10 4 1 2 f y y 2 4 5 5 5 5 11 1 x x m n n 4 4 1 5 3 4 11 2 x x f n n 2 4 5 6 4 4 11 3 1 2 m y y 4 4 5 5 4 4 11 4 1 2 f n n 2 4 5 6 4 4 12 1 x x m n n 4 4 4 5 x x 12 2 x x f n n 3 4 1 2 x x 12 3 1 2 f y y 4 4 1 5 x x 13 1 x x m n n 4 4 3 5 x x 13 2 x x f n n 4 8 2 5 x x 13 3 1 2 m y y 4 4 5 5 x x 13 4 1 2 f y n 4 4 5 5 x x 14 1 x x m n n x x x x x x 14 2 x x f n n x x x x x x 14 3 1 2 f y y 4 4 5 5 x x 14 4 1 2 f n n x x x x x x ;;;; run echo echo ======== echo Test 106 echo ======== echo show pedigrees list echo echo ======== echo Test 107 echo ======== echo show pedigrees echo echo ======== echo Test 108 echo ======== echo fre snp echo echo ======== echo Test 109 echo ======== echo set nhap 10 dis set iter 50 echo echo ======== echo Test 110 echo ======== echo hom lincl echo echo ======== echo Test 111 echo ======== echo mul lincl echo echo ======== echo Test 112 echo ======== echo ass lincl echo echo ======== echo Test 113 echo ======== echo mqls lincl 0.0001 echo echo ======== echo Test 114 echo ======== echo tdt lincl echo echo ======== echo Test 115 echo ======== echo tdt oneperfam clear echo echo Testing QTDT echo set seeds 12234 2323 13143 set loc trait quantitative set loc marker marker # # One hundred triad families # simulate pedigrees 100 2 1 1 run sim marker 0.6 0.4 if (marker=="1/1") then trait=rnorm else trait=rnorm+0.75 if (isfou) then trait=x echo echo ======== echo Test 116 echo ======== echo MENDEL Gametic competition model P=0.0155 echo QTDT Orthogonal model F=4.84 P=0.0301 echo tdt trait clear echo echo Testing conditional logistic regression: echo # # Matched case-control study data from # Trichopoulos et al. (1976) Br J Obs Gynaec 83: 645-650. # # coef exp(coef) se(coef) z p # spontaneous 1.99 7.29 0.352 5.63 1.8e-08 # induced 1.41 4.09 0.361 3.91 9.4e-05 # # Likelihood ratio test=53.1 on 2 df, p=2.87e-12 n= 248 # set locus education qua . 1 = 0-5 2= 6-11 3= 12+ set locus age qua . age in years set locus parity qua . count set locus induced qua . TOP 0=0 1=1 2=2+ set locus case qua . set locus spontaneous qua . miscarriage 0=0 1=1 2=2+ set locus stratum qua . matching stratum read pedigree inline # # strat id education age parity induced case spontaneous stratum 1 1 f1 m2 f 1 26 6 1 1 2 1 1 84 f1 m2 f 1 26 6 2 0 0 1 1 166 f1 m2 f 1 26 6 2 0 0 1 2 2 f1 m2 f 1 42 1 1 1 0 2 2 85 f1 m2 f 1 42 1 0 0 0 2 2 167 f1 m2 f 1 42 1 0 0 0 2 3 3 f1 m2 f 1 39 6 2 1 0 3 3 86 f1 m2 f 1 39 6 2 0 0 3 3 168 f1 m2 f 1 39 6 2 0 0 3 4 4 f1 m2 f 1 34 4 2 1 0 4 4 87 f1 m2 f 1 34 4 0 0 1 4 4 169 f1 m2 f 1 34 4 0 0 2 4 5 5 f1 m2 f 2 35 3 1 1 1 5 5 88 f1 m2 f 2 35 3 2 0 0 5 5 170 f1 m2 f 2 35 3 0 0 0 5 6 6 f1 m2 f 2 36 4 2 1 1 6 6 89 f1 m2 f 2 36 4 1 0 1 6 6 171 f1 m2 f 2 36 4 0 0 2 6 7 7 f1 m2 f 2 23 1 0 1 0 7 7 90 f1 m2 f 2 23 1 0 0 0 7 7 172 f1 m2 f 2 23 1 0 0 0 7 8 8 f1 m2 f 2 32 2 0 1 0 8 8 91 f1 m2 f 2 32 2 2 0 0 8 8 173 f1 m2 f 2 32 2 0 0 1 8 9 9 f1 m2 f 2 21 1 0 1 1 9 9 92 f1 m2 f 2 21 1 0 0 1 9 9 174 f1 m2 f 2 21 1 1 0 0 9 10 10 f1 m2 f 2 28 2 0 1 0 10 10 93 f1 m2 f 2 28 2 0 0 1 10 10 175 f1 m2 f 2 28 2 0 0 1 10 11 11 f1 m2 f 2 29 2 1 1 0 11 11 94 f1 m2 f 2 29 2 0 0 0 11 11 176 f1 m2 f 2 29 2 0 0 1 11 12 12 f1 m2 f 2 37 4 2 1 1 12 12 95 f1 m2 f 2 37 4 1 0 1 12 12 177 f1 m2 f 2 37 4 0 0 1 12 13 13 f1 m2 f 2 31 1 1 1 0 13 13 96 f1 m2 f 2 31 1 0 0 0 13 13 178 f1 m2 f 2 31 1 0 0 0 13 14 14 f1 m2 f 2 29 3 2 1 0 14 14 97 f1 m2 f 2 29 3 0 0 1 14 14 179 f1 m2 f 2 29 3 0 0 2 14 15 15 f1 m2 f 2 31 2 1 1 1 15 15 98 f1 m2 f 2 31 2 1 0 0 15 15 180 f1 m2 f 2 31 2 1 0 0 15 16 16 f1 m2 f 2 27 2 2 1 0 16 16 99 f1 m2 f 2 27 2 1 0 0 16 16 181 f1 m2 f 2 27 2 0 0 0 16 17 17 f1 m2 f 2 30 5 2 1 1 17 17 100 f1 m2 f 2 30 5 0 0 2 17 17 182 f1 m2 f 2 30 5 1 0 2 17 18 18 f1 m2 f 2 26 1 0 1 1 18 18 101 f1 m2 f 2 26 1 0 0 0 18 18 183 f1 m2 f 2 26 1 1 0 0 18 19 19 f1 m2 f 2 25 3 2 1 1 19 19 102 f1 m2 f 2 25 3 0 0 1 19 19 184 f1 m2 f 2 25 3 1 0 1 19 20 20 f1 m2 f 2 44 1 0 1 1 20 20 103 f1 m2 f 2 44 1 0 0 0 20 20 185 f1 m2 f 2 44 1 1 0 0 20 21 21 f1 m2 f 2 40 1 0 1 1 21 21 104 f1 m2 f 2 40 1 0 0 0 21 21 186 f1 m2 f 2 40 1 0 0 0 21 22 22 f1 m2 f 2 35 2 2 1 0 22 22 105 f1 m2 f 2 35 2 0 0 0 22 22 187 f1 m2 f 2 35 2 0 0 0 22 23 23 f1 m2 f 2 28 2 0 1 2 23 23 106 f1 m2 f 2 28 2 0 0 0 23 23 188 f1 m2 f 2 28 2 2 0 0 23 24 24 f1 m2 f 2 36 1 0 1 1 24 24 107 f1 m2 f 2 36 1 0 0 0 24 24 189 f1 m2 f 2 36 1 0 0 1 24 25 25 f1 m2 f 2 27 2 1 1 1 25 25 108 f1 m2 f 2 27 2 0 0 1 25 25 190 f1 m2 f 2 27 2 0 0 2 25 26 26 f1 m2 f 2 40 2 0 1 2 26 26 109 f1 m2 f 2 40 2 0 0 0 26 26 191 f1 m2 f 2 40 2 0 0 0 26 27 27 f1 m2 f 2 38 2 0 1 2 27 27 110 f1 m2 f 2 38 2 0 0 0 27 27 192 f1 m2 f 2 38 2 0 0 0 27 28 28 f1 m2 f 2 34 3 0 1 2 28 28 111 f1 m2 f 2 34 3 0 0 0 28 28 193 f1 m2 f 2 34 3 0 0 0 28 29 29 f1 m2 f 2 28 4 1 1 2 29 29 112 f1 m2 f 2 28 4 0 0 2 29 29 194 f1 m2 f 2 28 4 2 0 1 29 30 30 f1 m2 f 2 30 4 2 1 0 30 30 113 f1 m2 f 2 30 4 1 0 1 30 30 195 f1 m2 f 2 30 4 1 0 1 30 31 31 f1 m2 f 2 32 1 0 1 1 31 31 114 f1 m2 f 2 32 1 0 0 0 31 31 196 f1 m2 f 2 32 1 0 0 0 31 32 32 f1 m2 f 2 34 2 1 1 0 32 32 115 f1 m2 f 2 34 2 1 0 0 32 32 197 f1 m2 f 2 34 2 0 0 0 32 33 33 f1 m2 f 2 42 1 1 1 0 33 33 116 f1 m2 f 2 42 1 1 0 0 33 33 198 f1 m2 f 2 42 1 0 0 0 33 34 34 f1 m2 f 2 32 2 0 1 2 34 34 117 f1 m2 f 2 32 2 0 0 0 34 34 199 f1 m2 f 2 32 2 2 0 0 34 35 35 f1 m2 f 2 39 1 1 1 0 35 35 118 f1 m2 f 2 39 1 0 0 0 35 35 200 f1 m2 f 2 39 1 0 0 0 35 36 36 f1 m2 f 2 35 2 0 1 2 36 36 119 f1 m2 f 2 35 2 0 0 0 36 36 201 f1 m2 f 2 35 2 0 0 0 36 37 37 f1 m2 f 2 36 1 0 1 1 37 37 120 f1 m2 f 2 36 1 0 0 0 37 37 202 f1 m2 f 2 36 1 0 0 0 37 38 38 f1 m2 f 2 34 3 1 1 2 38 38 121 f1 m2 f 2 34 3 2 0 0 38 38 203 f1 m2 f 2 34 3 2 0 0 38 39 39 f1 m2 f 2 30 3 0 1 0 39 39 122 f1 m2 f 2 30 3 0 0 2 39 39 204 f1 m2 f 2 30 3 0 0 1 39 40 40 f1 m2 f 2 28 1 0 1 1 40 40 123 f1 m2 f 2 28 1 1 0 0 40 40 205 f1 m2 f 2 28 1 0 0 0 40 41 41 f1 m2 f 2 39 3 0 1 2 41 41 124 f1 m2 f 2 39 3 1 0 0 41 41 206 f1 m2 f 2 39 3 0 0 0 41 42 42 f1 m2 f 2 35 1 0 1 0 42 42 125 f1 m2 f 2 35 1 0 0 0 42 42 207 f1 m2 f 2 35 1 0 0 0 42 43 43 f1 m2 f 2 41 1 0 1 0 43 43 126 f1 m2 f 2 41 1 0 0 0 43 43 208 f1 m2 f 2 41 1 0 0 0 43 44 44 f1 m2 f 2 37 2 1 1 1 44 44 127 f1 m2 f 2 37 2 0 0 0 44 44 209 f1 m2 f 2 37 2 0 0 0 44 45 45 f1 m2 f 3 30 1 0 1 0 45 45 128 f1 m2 f 3 30 1 1 0 0 45 45 210 f1 m2 f 3 30 1 0 0 0 45 46 46 f1 m2 f 3 37 1 1 1 0 46 46 129 f1 m2 f 3 37 1 0 0 0 46 46 211 f1 m2 f 3 37 1 0 0 1 46 47 47 f1 m2 f 3 28 2 0 1 2 47 47 130 f1 m2 f 3 28 2 1 0 0 47 47 212 f1 m2 f 3 28 2 1 0 0 47 48 48 f1 m2 f 3 27 4 2 1 0 48 48 131 f1 m2 f 3 27 4 2 0 1 48 48 213 f1 m2 f 3 27 4 2 0 0 48 49 49 f1 m2 f 3 26 2 2 1 0 49 49 132 f1 m2 f 3 26 2 1 0 0 49 49 214 f1 m2 f 3 26 2 1 0 0 49 50 50 f1 m2 f 3 38 3 0 1 2 50 50 133 f1 m2 f 3 38 3 1 0 0 50 50 215 f1 m2 f 3 38 3 1 0 0 50 51 51 f1 m2 f 3 24 3 1 1 2 51 51 134 f1 m2 f 3 24 3 2 0 1 51 51 216 f1 m2 f 3 24 3 2 0 0 51 52 52 f1 m2 f 3 36 5 1 1 2 52 52 135 f1 m2 f 3 36 5 1 0 1 52 52 217 f1 m2 f 3 36 5 2 0 1 52 53 53 f1 m2 f 3 27 3 1 1 1 53 53 136 f1 m2 f 3 27 3 1 0 1 53 53 218 f1 m2 f 3 27 3 2 0 0 53 54 54 f1 m2 f 3 28 1 0 1 1 54 54 137 f1 m2 f 3 28 1 1 0 0 54 54 219 f1 m2 f 3 28 1 0 0 1 54 55 55 f1 m2 f 3 29 2 0 1 2 55 55 138 f1 m2 f 3 29 2 1 0 0 55 55 220 f1 m2 f 3 29 2 1 0 1 55 56 56 f1 m2 f 3 36 2 0 1 2 56 56 139 f1 m2 f 3 36 2 1 0 0 56 56 221 f1 m2 f 3 36 2 0 0 1 56 57 57 f1 m2 f 3 28 2 1 1 0 57 57 140 f1 m2 f 3 28 2 1 0 1 57 57 222 f1 m2 f 3 28 2 2 0 0 57 58 58 f1 m2 f 3 28 2 0 1 2 58 58 141 f1 m2 f 3 28 2 2 0 0 58 58 223 f1 m2 f 3 28 2 1 0 0 58 59 59 f1 m2 f 3 28 1 0 1 1 59 59 142 f1 m2 f 3 28 1 1 0 0 59 59 224 f1 m2 f 3 28 1 0 0 0 59 60 60 f1 m2 f 3 27 2 0 1 2 60 60 143 f1 m2 f 3 27 2 1 0 0 60 60 225 f1 m2 f 3 27 2 1 0 0 60 61 61 f1 m2 f 3 35 2 0 1 2 61 61 144 f1 m2 f 3 35 2 2 0 0 61 61 226 f1 m2 f 3 35 2 1 0 0 61 62 62 f1 m2 f 3 25 1 0 1 1 62 62 145 f1 m2 f 3 25 1 1 0 0 62 62 227 f1 m2 f 3 25 1 1 0 0 62 63 63 f1 m2 f 3 34 1 0 1 1 63 63 146 f1 m2 f 3 34 1 0 0 0 63 63 228 f1 m2 f 3 34 1 0 0 0 63 64 64 f1 m2 f 3 31 2 0 1 2 64 64 147 f1 m2 f 3 31 2 0 0 0 64 64 229 f1 m2 f 3 31 2 1 0 0 64 65 65 f1 m2 f 3 26 2 1 1 0 65 65 148 f1 m2 f 3 26 2 0 0 1 65 65 230 f1 m2 f 3 26 2 0 0 2 65 66 66 f1 m2 f 3 32 1 0 1 1 66 66 149 f1 m2 f 3 32 1 0 0 0 66 66 231 f1 m2 f 3 32 1 1 0 0 66 67 67 f1 m2 f 3 21 1 0 1 1 67 67 150 f1 m2 f 3 21 1 0 0 1 67 67 232 f1 m2 f 3 21 1 0 0 0 67 68 68 f1 m2 f 3 28 3 1 1 2 68 68 151 f1 m2 f 3 28 3 2 0 0 68 68 233 f1 m2 f 3 28 3 2 0 0 68 69 69 f1 m2 f 3 37 3 0 1 2 69 69 152 f1 m2 f 3 37 3 1 0 1 69 69 234 f1 m2 f 3 37 3 0 0 2 69 70 70 f1 m2 f 3 25 1 1 1 0 70 70 153 f1 m2 f 3 25 1 0 0 0 70 70 235 f1 m2 f 3 25 1 1 0 0 70 71 71 f1 m2 f 3 32 1 1 1 0 71 71 154 f1 m2 f 3 32 1 1 0 0 71 71 236 f1 m2 f 3 32 1 0 0 0 71 72 72 f1 m2 f 3 25 1 0 1 1 72 72 155 f1 m2 f 3 25 1 0 0 0 72 72 237 f1 m2 f 3 25 1 1 0 0 72 73 73 f1 m2 f 3 31 1 0 1 1 73 73 156 f1 m2 f 3 31 1 0 0 1 73 73 238 f1 m2 f 3 31 1 0 0 0 73 74 74 f1 m2 f 3 38 6 0 1 2 74 74 239 f1 m2 f 3 38 6 0 0 2 74 75 75 f1 m2 f 3 26 2 0 1 2 75 75 157 f1 m2 f 3 26 2 0 0 2 75 75 240 f1 m2 f 3 26 2 1 0 1 75 76 76 f1 m2 f 3 31 1 0 1 1 76 76 158 f1 m2 f 3 31 1 0 0 0 76 76 241 f1 m2 f 3 31 1 1 0 0 76 77 77 f1 m2 f 3 31 2 0 1 1 77 77 159 f1 m2 f 3 31 2 2 0 0 77 77 242 f1 m2 f 3 31 2 0 0 1 77 78 78 f1 m2 f 3 25 1 1 1 0 78 78 160 f1 m2 f 3 25 1 0 0 0 78 78 243 f1 m2 f 3 25 1 0 0 1 78 79 79 f1 m2 f 3 31 1 0 1 1 79 79 161 f1 m2 f 3 31 1 0 0 0 79 79 244 f1 m2 f 3 31 1 0 0 1 79 80 80 f1 m2 f 3 34 1 0 1 1 80 80 162 f1 m2 f 3 34 1 0 0 0 80 80 245 f1 m2 f 3 34 1 0 0 0 80 81 81 f1 m2 f 3 35 2 2 1 0 81 81 163 f1 m2 f 3 35 2 0 0 0 81 81 246 f1 m2 f 3 35 2 2 0 0 81 82 82 f1 m2 f 3 29 1 0 1 1 82 82 164 f1 m2 f 3 29 1 0 0 1 82 82 247 f1 m2 f 3 29 1 0 0 1 82 83 83 f1 m2 f 3 23 1 0 1 1 83 83 165 f1 m2 f 3 23 1 0 0 1 83 83 248 f1 m2 f 3 23 1 0 0 1 83 ;;;; run recast case affection head echo echo ======== echo Test 117 echo ======== echo echo ========================================================== echo Matched case-control study data from echo Trichopoulos et al. (1976) Br J Obs Gynaec 83: 645-650. echo echo Results from R 2.7.0 are: echo coef exp(coef) se(coef) z p echo spontaneous 1.985876 7.29 0.352443 5.63 1.8e-08 echo induced 1.409012 4.09 0.360712 3.91 9.4e-05 echo echo Likelihood ratio test=53.15424 on 2 df, p=2.87e-12 n= 248 echo Score test=48.43865 echo echo ========================================================== echo clr case = spontaneous induced echo clear ! ! Allelic association but only weak evidence for linkage to the ! Apolipoprotein locus in late-onset Swedish Alzheimer families ! ! Liu et al Am J Med Genet (Neuropsychiatr Genet) 1996; 67: 306-311 ! ! 15 families as drawn Figure 1 (pp 307-308) ! set loc ad aff set loc onset qua set loc apoe mar read ped inline F100 101 x x m n x x x F100 102 x x f y x x x F100 201 101 102 f y x x x F100 202 x x m n x x x F100 203 101 102 m y 70 4 4 F100 204 x x f n 82 3 3 F100 205 101 102 m y 72 3 4 F100 301 202 201 f n 46 4 4 F100 302 203 204 m n 49 3 4 F100 303 203 204 m n 44 3 4 F102 101 x x m n x x x F102 102 x x f y x x x F102 201 x x m n x x x F102 202 101 102 f n 91 3 3 F102 203 101 102 f y 83 3 3 F102 204 x x m n x x x F102 301 201 202 f n x x x F102 302 x x m n x x x F102 303 204 203 f n 63 3 3 F102 304 x x f n 60 3 3 F102 305 204 203 m y 52 3 4 F102 306 x x m n x x x F102 307 204 203 f n 55 3 4 F102 401 302 303 m n x x x F102 402 302 303 f n x x x F102 403 302 303 m n x x x F102 404 305 304 m n 40 3 3 F102 405 306 307 f n x x x F102 406 306 307 m n x x x F104 101 x x m n x x x F104 102 x x f n x x x F104 201 101 102 f y x x x F104 202 101 102 f n x x x F104 203 101 102 f n x x x F104 204 x x m n x x x F104 205 101 102 m n x x x F104 206 x x f n x x x F104 207 101 102 f y 79 3 4 F104 208 x x m n x x x F104 209 101 102 m y x x x F104 210 x x f n x x x F104 211 101 102 f y 79 3 4 F104 212 101 102 m n x x x F104 213 101 102 m n x x x F104 214 101 102 f n x x x F104 215 101 102 f n 77 3 4 F104 301 204 203 m n x x x F104 302 204 203 f n x x x F104 303 205 206 f n x x x F104 304 205 206 f n x x x F104 305 208 207 f n 71 3 3 F104 306 x x m n x x x F104 307 208 207 f n 67 3 3 F104 308 x x m n x x x F104 309 209 210 f n x x x F104 310 x x m n x x x F104 311 209 210 f n x x x F104 312 x x m n x x x F104 401 306 305 f n x x x F104 402 306 305 m n x x x F104 403 308 307 f n x x x F104 404 308 307 m n x x x F104 405 310 309 f n x x x F104 406 312 311 f n x x x F106 101 x x m n x x x F106 102 x x f n x x x F106 201 101 102 m y x x x F106 202 x x f n 86 3 3 F106 203 101 102 f y 80 2 4 F106 204 x x m n x x x F106 205 101 102 f y x x x F106 206 x x m n x x x F106 207 101 102 f y x x x F106 208 101 102 f y 60 4 4 F106 209 x x m n x x x F106 210 101 102 m y 70 3 4 F106 211 x x f n 80 3 3 F106 212 101 102 m n 80 2 3 F106 213 x x f n 79 2 4 F106 301 201 202 m n 63 3 4 F106 302 201 202 m n x x x F106 303 201 202 f n 61 3 3 F106 304 204 203 m n 51 3 4 F106 305 204 203 f n 51 2 3 F106 306 206 207 m n x x x F106 307 206 207 f n x x x F106 308 209 208 f n 60 3 4 F106 309 210 211 f n 55 3 4 F106 310 210 211 m n 50 3 3 F106 311 210 211 m n 48 3 3 F106 312 212 213 m n 49 2 3 F106 313 212 213 f n x x x F107 101 x x m n x x x F107 102 x x f y x x x F107 201 101 102 m n 84 3 3 F107 202 101 102 f y x x x F107 203 101 102 f y 69 3 4 F107 204 101 102 f n 63 4 4 F107 205 101 102 m y 67 3 4 F107 206 101 102 m n 70 4 4 F107 207 101 102 f y 58 4 4 F107 208 101 102 f y 57 3 4 F107 209 101 102 m n 59 3 3 F118 101 x x m n x x x F118 102 x x f y x x x F118 201 101 102 f y x x x F118 202 101 102 m n x x x F118 203 101 102 f y x x x F118 204 101 102 m n 91 3 4 F118 205 101 102 m n x x x F118 206 101 102 m n x x x F118 207 x x f n x x x F118 208 101 102 f y x x x F118 209 x x m n x x x F118 210 101 102 f y 76 4 4 F118 211 x x m n x x x F118 212 101 102 f y x x x F118 213 x x m n x x x F118 214 101 102 f y 60 4 4 F118 215 x x m n x x x F118 301 206 207 m n x x x F118 302 206 207 m n x x x F118 303 209 208 f n x x x F118 304 209 208 f n 39 3 3 F118 305 211 210 f n x x x F118 306 213 212 f n x x x F118 307 213 212 f n x x x F118 308 213 212 f n 46 4 4 F118 309 215 214 m n x x x F118 310 215 214 m n x x x F118 311 215 214 m n x x x F118 312 215 214 f n x x x F118 313 215 214 f n x x x F133 101 x x m n x x x F133 102 x x f y x x x F133 201 101 102 f y x x x F133 202 x x m n x x x F133 203 101 102 m y x x x F133 204 x x f n x x x F133 301 202 201 f n x x x F133 302 202 201 m y x x x F133 303 x x f n x x x F133 304 202 201 m y x x x F133 305 202 201 m y x x x F133 306 202 201 m y 76 3 4 F133 307 202 201 m n x x x F133 308 202 201 f n x x x F133 309 202 201 f n 60 3 3 F133 310 203 204 m n 76 2 4 F133 311 203 204 m n 71 2 3 F133 312 203 204 m y 61 4 4 F133 313 203 204 m n 67 2 3 F133 401 302 303 m n x x x F151 101 x x m n x x x F151 102 x x f y x x x F151 201 x x f n 80 3 3 F151 202 101 102 m y 76 3 3 F151 203 101 102 m x 78 3 3 F151 204 x x f n 72 3 3 F151 205 101 102 m y 67 3 4 F151 206 x x f n 74 3 3 F151 207 101 102 m y 60 3 4 F151 208 x x f n 69 3 3 F151 209 101 102 m n 74 3 3 F151 210 x x f n x x x F151 211 101 102 f n 71 3 3 F151 212 x x m n x x x F151 213 101 102 m x 68 3 4 F151 214 x x f n 72 4 4 F151 215 101 102 m n x x x F151 301 202 201 f n 59 3 3 F151 302 x x m n x x x F151 303 203 204 m n 46 3 3 F151 304 203 204 m n 44 3 3 F151 305 205 206 m n x x x F151 306 205 206 f n 50 3 3 F151 307 207 208 f n 43 3 3 F151 308 209 210 f n 45 3 4 F151 309 209 210 f n 41 3 4 F151 310 x x f n x x x F151 311 212 211 m n 52 3 3 F151 312 212 211 f n 47 3 3 F151 313 x x m n 50 3 3 F151 314 213 214 f n 36 4 4 F151 315 213 214 f n 31 3 4 F151 401 302 301 m n 36 3 3 F151 402 311 310 f n 31 3 3 F151 403 313 312 f n 25 3 3 F163 101 x x m n x x x F163 102 x x f y x x x F163 201 101 102 f n 94 3 3 F163 202 x x m n x x x F163 203 101 102 m n x x x F163 204 x x f n x x x F163 205 101 102 f y 73 3 4 F163 206 x x m n x x x F163 207 101 102 f n x x x F163 208 x x m n x x x F163 209 101 102 f y 76 3 3 F163 210 x x m n x x x F163 211 101 102 f y 76 3 4 F163 212 x x m n x x x F163 213 101 102 f n 76 3 4 F163 214 x x m n x x x F163 215 101 102 f y 59 3 4 F163 216 x x m n x x x F163 301 202 201 m n 67 3 3 F163 302 202 201 f n 71 3 3 F163 303 202 201 f n 73 3 3 F163 304 203 204 m n 50 3 3 F163 305 203 204 m n x x x F163 306 206 205 f n 56 3 4 F163 307 206 205 f n 55 3 3 F163 308 206 205 m n 54 4 4 F163 309 206 205 f n 52 3 3 F163 310 206 205 m n 51 3 4 F163 311 206 205 m n 49 3 4 F163 312 208 207 m n 53 3 4 F163 313 210 209 m n 47 3 4 F163 314 210 209 f n 44 3 4 F163 315 212 211 m n 53 2 4 F163 316 214 213 f n 43 3 4 F163 317 214 213 m n 48 3 3 F163 318 214 213 m n 35 3 4 F163 319 216 215 f n 47 3 3 F163 320 216 215 f n 35 3 4 F164 101 x x m n x x x F164 102 x x f n x x x F164 201 101 102 m n x x x F164 202 101 102 f y x x x F164 203 101 102 m n x x x F164 204 101 102 m n x x x F164 205 101 102 f n x x x F164 206 101 102 m n x 3 3 F164 207 101 102 f y 65 3 4 F164 208 x x m n x x x F164 209 101 102 f n x x x F164 210 101 102 f y 67 3 4 F164 211 101 102 m n 57 3 4 F164 212 101 102 f n 55 3 4 F164 213 101 102 f n 50 3 3 F164 214 101 102 m y x x x F164 301 208 207 f n x x x F164 302 208 207 f n x x x F175 101 x x m y x x x F175 102 x x f n x x x F175 201 101 102 m n x x x F175 202 x x f n x x x F175 301 201 202 m y 69 2 3 F175 302 201 202 m y 62 3 3 F175 303 201 202 m y 60 3 3 F175 304 201 202 m n 70 3 3 F175 305 201 202 m n 69 2 3 F175 306 201 202 m n 61 2 4 F176 101 x x m n x x x F176 102 x x f y x x x F176 201 x x m n x x x F176 202 101 102 f y x x x F176 203 101 102 f y 65 3 3 F176 301 201 202 f y 65 4 4 F176 302 201 202 f y x x x F176 303 201 202 m y 65 4 4 F176 304 201 202 m y 72 4 4 F176 305 201 202 f n 70 4 4 F176 306 201 202 f n 66 3 4 F176 307 201 202 m x 65 3 4 F176 308 201 202 m n 61 3 4 F197 101 x x m n x x x F197 102 x x f y x x x F197 201 101 102 m n x x x F197 202 x x f n x x x F197 203 101 102 m y 65 3 4 F197 204 101 102 f n x x x F197 205 101 102 m n x x x F197 206 101 102 f y 72 3 3 F197 207 x x m n 84 3 3 F197 208 101 102 m n x x x F197 209 101 102 m n 74 3 4 F197 210 x x f n x x x F197 211 101 102 m n x x x F197 212 101 102 f n 71 3 3 F197 213 101 102 f n 69 3 3 F197 214 x x m n x x x F197 215 101 102 m y 61 3 4 F197 216 x x f n 62 2 4 F197 217 101 102 f n x x x F197 301 203 202 m n 49 3 3 F197 302 207 206 f n 52 3 3 F197 303 207 206 f n 51 3 3 F197 304 207 206 m n 48 3 3 F197 305 207 206 m n 47 3 3 F197 306 209 210 f n 47 3 3 F197 307 214 213 m n 37 3 3 F197 308 215 216 f n 35 4 4 F197 309 215 216 m n 29 2 3 F204 101 x x m y x x x F204 102 x x f n x x x F204 201 101 102 f y 69 4 4 F204 202 x x m n x x x F204 203 x x m n x x x F204 204 101 102 f y 70 4 4 F204 205 101 102 f y 72 3 4 F204 206 101 102 m y x x x F204 207 101 102 m n x x x F204 208 x x m n x x x F204 209 101 102 f n 71 4 4 F204 210 101 102 f n 66 3 4 F204 301 202 201 f n 47 3 4 F204 302 202 201 f n 48 3 4 F204 303 203 204 m n 46 3 4 F204 304 203 204 m n 46 3 4 F204 305 208 209 m n 34 3 4 F204 306 208 209 m n 36 3 4 F205 101 x x m y x x x F205 102 x x f n x x x F205 201 x x f n x x x F205 202 101 102 m y x x x F205 203 101 102 f n x x x F205 301 202 201 f y 67 3 4 F205 302 x x m n x x x F205 303 202 201 f y 72 3 4 F205 304 202 201 f y 70 3 4 F205 305 x x m n x x x F205 306 202 201 m n 73 3 4 F205 307 x x m n x x x F205 308 202 201 f y 68 3 4 F205 309 202 201 f n 67 3 4 F205 401 302 301 m n 48 4 4 F205 402 302 301 m n 46 4 4 F205 403 305 304 m n 49 3 4 F205 404 305 304 m n 55 3 4 F205 405 307 308 m n 47 3 3 F205 406 307 308 f n 51 3 3 F205 407 307 308 m n 57 3 3 ;;;; run echo echo ======== echo Test 118 echo ======== sdt ad echo echo ======== echo Test 119 echo ======== ass ad clear echo echo Testing FBAT type statistic versus examples of the different types echo of nuclear family: echo set ple -1 silent set seeds 1324 12345 15125 set loc trait aff set loc marker mar read ped inline table1.1 1 x x m x A/A table1.1 2 x x f x x/x table1.1 3 1 2 m y A/A table1.1 4 1 2 m n A/A table1.2 1 x x m x A/A table1.2 2 x x f x x/x table1.2 3 1 2 m y A/A table1.2 4 1 2 m n A/B table1.2 5 1 2 m n A/B table1.3 1 x x m x A/A table1.3 2 x x f x x/x table1.3 3 1 2 m y A/B table1.3 4 1 2 m n A/C table1.3 5 1 2 m n A/C table2.1 1 x x m x A/B table2.1 2 x x f x x/x table2.1 3 1 2 m y A/A table2.1 4 1 2 m y A/A table2.2 1 x x m x A/B table2.2 2 x x f x x/x table2.2 3 1 2 m y A/A table2.2 4 1 2 m y A/A table2.2 5 1 2 m y A/A table2.2 6 1 2 m n A/B table2.2 7 1 2 m n A/B table2.3 1 x x m x A/B table2.3 2 x x f x x/x table2.3 3 1 2 m y A/A table2.3 4 1 2 m n B/B table2.3 5 1 2 m n B/B table2.4 1 x x m x A/B table2.4 2 x x f x x/x table2.4 3 1 2 m y A/C table2.4 4 1 2 m y B/C table2.4 5 1 2 m y B/C table2.4 6 1 2 m y B/C table2.5 1 x x m x A/B table2.5 2 x x f x x/x table2.5 3 1 2 m y A/B table2.5 4 1 2 m y A/C table2.5 5 1 2 m y A/C table2.5 6 1 2 m n B/C table2.6 1 x x m x A/B table2.6 2 x x f x x/x table2.6 3 1 2 m y A/A table2.6 4 1 2 m y A/A table2.6 5 1 2 m n A/C table2.6 6 1 2 m n B/C table2.7 1 x x m x A/B table2.7 2 x x f x x/x table2.7 3 1 2 m y A/C table2.7 4 1 2 m n B/D table2.7 5 1 2 m n B/C table3.2 1 x x m x x/x table3.2 2 x x f x x/x table3.2 3 1 2 m y A/A table3.2 4 1 2 m y A/A table3.2 5 1 2 m n A/B table3.2 6 1 2 m n A/B table3.2 7 1 2 m n A/B table3.3 1 x x m x x/x table3.3 2 x x f x x/x table3.3 3 1 2 m y A/A table3.3 4 1 2 m n A/B table3.3 5 1 2 m n B/B table3.3 6 1 2 m n B/B table3.4 1 x x m x x/x table3.4 2 x x f x x/x table3.4 3 1 2 m y A/B table3.4 4 1 2 m y A/C table3.4 5 1 2 m n B/C table3.4 6 1 2 m n B/C table3.5 1 x x m x x/x table3.5 2 x x f x x/x table3.5 3 1 2 m y A/B table3.5 4 1 2 m n A/C table3.6 1 x x m x x/x table3.6 2 x x f x x/x table3.6 3 1 2 m y A/B table3.6 4 1 2 m n B/C table3.6 5 1 2 m n B/C table3.6 6 1 2 m n B/C table3.6 7 1 2 m n B/C table3.7 1 x x m x x/x table3.7 2 x x f x x/x table3.7 3 1 2 m y A/C table3.7 4 1 2 m n B/C table3.7 5 1 2 m n B/D table3.7 6 1 2 m n B/D ;;;; run macro testfbat sel ped table%1 set ple 1 ass trait set ple -1 uns ;;;; set iter 5000 echo echo ======== echo Test 120 echo ======== echo echo Family type 1.1 echo Expect No useful sibships testfbat 1.1 echo echo ======== echo Test 121 echo ======== echo echo Family type 1.2 echo Expect A 2.0000 E=1.5000 V= 0.2500 -0.2500 echo Expect B 0.0000 E=0.5000 V= -0.2500 0.2500 testfbat 1.2 echo echo ======== echo Test 122 echo ======== echo echo Family type 1.3 echo Expect A 1.0000 E=1.0000 V=0.0000 0.0000 0.0000 echo Expect B 1.0000 E=0.5000 V=0.0000 0.2500 -0.2500 echo Expect C 0.0000 E=0.5000 V=0.0000 -0.2500 0.2500 testfbat 1.3 echo echo ======== echo Test 123 echo ======== echo echo Family type 2.1 echo Expect No useful sibships testfbat 2.1 echo echo ======== echo Test 124 echo ======== echo echo Family type 2.2 echo Expect A 6.0000 E=4.8000 V= 0.3600 -0.3600 echo Expect B 0.0000 E=1.2000 V=-0.3600 0.3600 testfbat 2.2 echo echo ======== echo Test 125 echo ======== echo echo Family type 2.3 echo Expect A 2.0000 E=1.0000 V= 0.7778 -0.7778 echo Expect B 0.0000 E=1.0000 V=-0.7778 0.7778 testfbat 2.3 echo echo ======== echo Test 126 echo ======== echo echo Family type 2.4 echo Expect A 1.0000 E=2.0000 V= 1.0000 -1.0000 0.0000 echo Expect B 3.0000 E=2.0000 V=-1.0000 1.0000 0.0000 echo Expect C 4.0000 E=4.0000 V= 0.0000 0.0000 0.0000 testfbat 2.4 echo echo ======== echo Test 127 echo ======== echo echo Family type 2.5 echo Expect A 3.0000 E=2.1094 V= 0.5662 -0.3245 -0.2417 echo Expect B 1.0000 E=2.1094 V=-0.3245 0.5662 -0.2417 echo Expect C 2.0000 E=1.7812 V=-0.2417 -0.2417 0.4834 testfbat 2.5 echo echo ======== echo Test 128 echo ======== echo echo Family type 2.6 echo Expect A 4.0000 E=2.2375 V= 0.9436 -0.4864 -0.4572 echo Expect B 0.0000 E=0.8375 V=-0.4864 0.4486 0.0378 echo Expect C 0.0000 E=0.9250 V=-0.4572 0.0378 0.4194 testfbat 2.6 echo echo ======== echo Test 129 echo ======== echo echo Family type 2.7 echo Expect A 1.0000 E=0.5000 V= 0.2500 -0.2500 0.0000 0.0000 echo Expect B 0.0000 E=0.5000 V=-0.2500 0.2500 0.0000 0.0000 echo Expect C 1.0000 E=0.5000 V= 0.0000 0.0000 0.2500 -0.2500 echo Expect D 0.0000 E=0.5000 V= 0.0000 0.0000 -0.2500 0.2500 testfbat 2.7 echo echo ======== echo Test 130 echo ======== echo echo Family type 3.2 echo Expect A 4.0000 E=2.8000 V= 0.3600 -0.3600 echo Expect B 0.0000 E=1.2000 V=-0.3600 0.3600 testfbat 3.2 echo echo ======== echo Test 131 echo ======== echo echo Family type 3.3 echo Expect A 2.0000 E=1.0000 V= 0.6727 -0.6727 echo Expect B 0.0000 E=1.0000 V=-0.6727 0.6727 testfbat 3.3 echo echo ======== echo Test 132 echo ======== echo echo Family type 3.4 echo Expect A 2.0000 E=1.3333 V= 0.3333 -0.1667 -0.1667 echo Expect B 1.0000 E=1.3333 V=-0.1667 0.3333 -0.1667 echo Expect C 1.0000 E=1.3333 V=-0.1667 -0.1667 0.3333 testfbat 3.4 echo echo ======== echo Test 133 echo ======== echo echo Family type 3.5 echo Expect A 1.0000 E=1.0000 V=0.0000 0.0000 0.0000 echo Expect B 1.0000 E=0.5000 V=0.0000 0.2500 -0.2500 echo Expect C 0.0000 E=0.5000 V=0.0000 -0.2500 0.2500 testfbat 3.5 echo echo ======== echo Test 134 echo ======== echo echo Family type 3.6 echo Expect A 1.0000 E=0.5000 V= 0.2500 0.0000 -0.2500 echo Expect B 1.0000 E=1.0000 V= 0.0000 0.0000 0.0000 echo Expect C 0.0000 E=0.5000 V=-0.2500 0.0000 0.2500 testfbat 3.6 echo echo ======== echo Test 135 echo ======== echo echo Family type 3.7 echo Expect A 1.0000 E=0.5000 V= 0.2500 -0.2500 0.0000 0.0000 echo Expect B 0.0000 E=0.5000 V=-0.2500 0.2500 0.0000 0.0000 echo Expect C 1.0000 E=0.5000 V= 0.0000 0.0000 0.2500 -0.2500 echo Expect D 0.0000 E=0.5000 V= 0.0000 0.0000 -0.2500 0.2500 testfbat 3.7 clear echo echo Testing GPEs: echo set ple -1 set seeds 1324 1345 15125 set loc published qua read pedigree inline hops 1 0 0 1 0.197 hops 2 0 0 2 0.099 hops 3 0 0 1 0.109 hops 4 0 0 2 0.109 hops 6 0 0 2 0.105 hops 7 0 0 1 0.113 hops 13 0 0 1 x hops 14 0 0 2 x hops 17 0 0 1 0.061 hops 18 0 0 2 0.055 hops 24 0 0 2 x hops 25 0 0 1 x hops 26 0 0 2 x hops 31 0 0 1 x hops 32 0 0 2 x hops 36 0 0 2 x hops 37 0 0 1 x hops 39 0 0 1 x hops 41 0 0 1 x hops 42 0 0 2 x hops 50 0 0 2 x hops 51 0 0 1 x hops 56 0 0 2 0.057 hops 57 0 0 1 0.059 hops 58 0 0 2 0.055 hops 70 0 0 2 x hops 96 0 0 2 x hops 100 0 0 1 x hops 101 0 0 2 x hops 270 0 0 1 x hops 271 0 0 1 x hops 108 0 0 2 x hops 113 0 0 1 x hops 114 0 0 2 x hops 125 0 0 2 x hops 126 0 0 1 x hops 148 0 0 1 x hops 162 0 0 1 x hops 172 0 0 1 x hops 173 0 0 2 x hops 199 0 0 1 x hops 200 0 0 2 x hops 201 0 0 1 x hops 204 0 0 2 x hops 206 0 0 2 x hops 220 0 0 2 x hops 231 0 0 2 x hops 249 0 0 2 x hops 5 3 4 1 x hops 8 7 6 2 x hops 9 5 8 1 x hops 10 9 2 2 x hops 11 1 10 1 x hops 12 7 6 2 x hops 15 13 14 1 x hops 16 15 12 2 x hops 19 17 18 1 x hops 20 3 4 2 x hops 21 19 20 1 x hops 22 21 16 2 x hops 23 7 6 1 x hops 27 25 26 1 x hops 28 27 24 2 x hops 29 23 28 1 x hops 30 29 22 2 x hops 33 31 32 1 x hops 34 27 24 2 x hops 35 33 34 1 x hops 38 37 36 2 x hops 40 39 38 2 x hops 43 41 42 1 x hops 44 13 14 2 x hops 45 43 44 1 x hops 46 45 40 2 x hops 47 35 46 1 x hops 48 47 30 2 x hops 49 11 48 1 x hops 52 51 50 2 x hops 53 3 4 1 x hops 54 17 18 2 x hops 55 53 54 1 x hops 59 57 58 1 x hops 60 59 56 2 x hops 61 55 60 1 x hops 62 61 52 2 x hops 63 21 16 1 x hops 64 5 8 2 x hops 65 63 64 1 x hops 66 65 62 2 x hops 67 49 66 1 x hops 68 1 10 2 x hops 69 61 52 1 x hops 71 57 58 1 x hops 72 71 70 2 x hops 73 17 18 1 x hops 74 73 72 2 x hops 75 37 36 1 x hops 76 7 6 2 x hops 77 59 76 2 x hops 78 75 77 1 x hops 79 78 74 2 x hops 80 71 70 1 x hops 81 80 34 1 x hops 82 5 8 2 x hops 83 81 82 1 x hops 84 83 79 2 x hops 85 69 84 1 x hops 86 85 68 2 x hops 87 67 86 1 x hops 88 81 82 2 x hops 89 73 72 1 x hops 90 31 32 1 x hops 91 90 60 2 x hops 92 89 91 1 x hops 93 92 88 2 x hops 94 71 70 2 x hops 95 23 94 1 x hops 97 95 96 1 x hops 98 7 6 2 x hops 99 71 98 2 x hops 102 100 101 1 x hops 103 102 99 2 x hops 104 97 103 1 x hops 105 75 77 2 x hops 106 270 42 2 x hops 107 271 106 1 x hops 109 107 108 1 x hops 110 109 105 2 x hops 111 100 101 1 x hops 112 17 18 2 x hops 115 113 114 1 x hops 116 115 112 2 x hops 117 111 116 1 x hops 118 117 40 1 x hops 119 118 110 2 x hops 120 104 119 1 x hops 121 120 93 2 x hops 122 1 10 1 x hops 123 63 64 2 x hops 124 73 72 1 x hops 127 126 125 2 x hops 128 7 6 1 x hops 129 128 127 2 x hops 130 124 129 1 x hops 131 39 38 2 x hops 132 59 56 1 x hops 133 132 131 2 x hops 134 130 133 1 x hops 135 134 123 2 x hops 136 122 135 1 x hops 137 136 121 2 x hops 138 87 137 1 x hops 139 122 135 1 x hops 140 120 93 2 x hops 141 139 140 1 x hops 142 85 68 2 x hops 143 49 66 1 x hops 144 143 142 2 x hops 145 141 144 2 x hops 163 43 44 2 x hops 191 33 34 1 x hops 192 5 8 2 x hops 193 191 192 1 x hops 194 162 163 2 x hops 202 201 200 2 x hops 203 199 202 1 x hops 205 17 18 1 x hops 207 113 114 1 x hops 208 207 206 2 x hops 209 205 208 1 x hops 218 61 52 1 x hops 219 172 173 2 x hops 221 162 220 1 x hops 222 221 219 2 x hops 223 53 54 2 x hops 224 203 223 1 x hops 225 224 222 2 x hops 226 218 225 1 x hops 227 1 10 2 x hops 228 226 227 1 x hops 229 209 204 2 x hops 230 73 72 1 x hops 232 230 231 1 x hops 233 232 229 2 x hops 234 172 173 2 x hops 235 78 234 1 x hops 236 235 233 2 x hops 237 134 123 1 x hops 238 237 236 2 x hops 239 228 238 1 x hops 240 193 194 2 x hops 241 132 131 1 x hops 242 115 112 2 x hops 243 3 4 1 x hops 244 126 125 2 x hops 245 243 244 1 x hops 246 245 242 2 x hops 247 241 246 1 x hops 248 75 77 2 x hops 250 148 249 1 x hops 251 250 248 2 x hops 252 247 251 1 x hops 253 252 240 2 x hops 254 92 88 1 x hops 255 134 123 2 x hops 256 254 255 1 x hops 257 256 253 2 x hops 258 239 257 1 x hops 259 237 236 1 x hops 260 226 227 2 x hops 261 259 260 1 x hops 262 237 236 2 x hops 263 252 240 1 x hops 264 263 262 2 x hops 265 104 119 1 x hops 266 218 225 2 x hops 267 265 266 1 x hops 268 267 264 2 x hops 269 261 268 2 x hops 273 138 145 1 x hops 275 258 269 1 x ;;;; run set loc hops mar echo echo ======== echo Test 136 echo ======== echo edit hops {273 275} hops "2/2" set freq hops 1 0.99 2 0.01 hops=hops+0 set iter 1000 set loc risk qua gpe hops risk set loc carrier1 qua carrier1 = 1-0.5*risk gpe hops mcmc risk set loc carrier2 qua carrier2 = 1-0.5*risk drop hops risk echo echo ======== echo Test 137 echo ======== echo echo ====================================================== echo Table 1 from Lin, Thompson and Wijsman (1994). Ann Hum echo Genet 58: 353. Estimated posterior carrier probabilities, echo echo conditional on the data, obtained by running echo the heated-Metropolis algorithm, for the Hutterite pedigree echo and data in Figure 2 echo (Listed are only those founders whose posterior probabilities echo of being carriers are estimated to be more than 5\%). echo Founder Carrier Standard echo label probability error echo 1 0.197 0.012 echo 2 0.099 0.005 echo 3 0.109 0.006 echo 4 0.109 0.006 echo 6 0.105 0.010 echo 7 0.113 0.010 echo 17 0.061 0.005 echo 18 0.055 0.005 echo 56 0.057 0.004 echo 57 0.059 0.003 echo 58 0.055 0.004 echo echo ====================================================== print published clear echo echo echo Testing segregation analysis: echo echo Alaskan hypercholesterolemia pedigree used for example 12 echo in the MENDEL manual [Lange 1986]: age, log(sChol) echo echo Schrott HG, Goldstein JL, Hazzard WR, McGoodwin MM, Motulsky AG: echo Familial hypercholesterolemia in a large kindred: Evidence for a echo monogenic mechanism. Ann. Int. Med. 76:711-720, 1972 echo set locus age qua set locus logChol qua read pedigree inline 1 101 x x f 62. x 1 102 x x m 87. 5.313206 1 201 102 101 f 38. x 1 202 x x m 51. 5.690359 1 203 102 101 m 47. 5.313206 1 204 x x f 36. 5.545177 1 205 102 101 m 41. x 1 206 x x f 41. 5.655992 1 207 102 101 m 38. x 1 208 x x f 38. 5.030438 1 209 102 101 f 38. x 1 210 x x m 38. x 1 212 102 101 m 41. 5.899897 1 213 x x f 35. 5.288267 1 214 102 101 f 39. 5.700444 1 215 x x m 47. 5.463832 1 216 102 101 m 38. 6.171701 1 217 x x f 36. 5.446737 1 218 102 101 f 36. 6.104793 1 219 x x m 35. 5.746203 1 220 102 101 m 35. 5.937536 1 221 x x f 28. 5.347108 1 222 102 101 m 32. 5.929589 1 223 x x f 27. 5.105945 1 224 102 101 m 30. 5.505332 1 225 x x f 26. 5.375278 1 226 x x m 28. x 1 227 102 101 f 28. 5.262690 1 228 x x m 48. 5.497168 1 229 102 101 m 27. 6.030685 1 230 102 101 m 26. 5.236442 1 231 102 101 m 24. 5.347108 1 232 102 101 m 22. 5.283204 1 233 x x f 19. 4.969813 1 301 202 201 m 31. 6.045005 1 302 x x f 30. 5.501258 1 303 202 201 m 30. 5.398163 1 304 x x f 29. 5.602119 1 305 202 201 m 29. 5.393628 1 306 x x f 26. 5.241747 1 307 202 201 m 26. 6.052089 1 308 202 201 m 25. 5.488938 1 309 202 201 f 24. 5.802118 1 311 202 201 f 22. 6.388561 1 312 x x m 23. 5.241747 1 313 202 201 f 21. 6.086775 1 314 x x m 21. x 1 315 202 201 m 20. 5.968708 1 316 202 201 m 16. 5.638355 1 317 202 201 f 15. 5.899897 1 318 203 204 f 12. 5.529429 1 319 203 204 f 11. 5.521461 1 320 203 204 m 10. 5.455321 1 322 203 204 m 6. 5.308268 1 323 205 206 f 25. 5.327876 1 325 205 206 m 22. 5.153292 1 326 207 208 m 20. 5.929589 1 327 207 208 m 17. 5.758902 1 328 210 209 f 22. 5.298317 1 329 210 209 f 20. 5.111988 1 330 x x m 20. x 1 331 210 209 f 12. 5.398163 1 332 210 209 m 8. 5.484797 1 333 210 209 f 6. 5.298317 1 334 212 213 m 20. 5.225747 1 335 212 213 f 17. 5.549076 1 336 212 213 m 16. 5.686975 1 337 212 213 m 15. 5.365976 1 338 212 213 f 4. 5.820083 1 339 215 214 m 20. 5.780744 1 340 215 214 f 19. 5.634790 1 341 215 214 f 15. 5.942799 1 342 215 214 m 12. 5.442418 1 343 215 214 f 10. 5.910797 1 344 216 217 m 18. 5.164786 1 345 216 217 f 17. 5.170484 1 346 216 217 f 16. 5.899897 1 347 216 217 m 14. 5.192957 1 348 216 217 m 13. 5.192957 1 349 216 217 m 11. 5.733341 1 350 216 217 f 10. 6.070738 1 351 216 217 f 6. 5.147494 1 352 216 217 m 1. 5.252273 1 353 219 218 m 16. 5.768321 1 354 219 218 f 13. 5.932245 1 355 219 218 m 10. 6.021023 1 356 219 218 f 4. 6.118097 1 357 220 221 m 8. 5.337538 1 358 220 221 m 6. 6.023448 1 359 220 221 f 5. 5.579730 1 360 222 223 f 8. 5.198497 1 361 222 223 f 6. 5.924256 1 362 224 225 f 6. 5.389072 1 363 224 225 f 4. 5.393628 1 364 224 225 m 2. 5.267858 1 365 226 227 f 5. 5.365976 1 367 232 233 m 2. 5.075174 1 368 232 233 f 1. 5.505332 1 401 301 302 m 12. 5.831882 1 402 301 302 f 9. 5.365976 1 403 301 302 m 5. 5.323010 1 404 303 304 f 7. 5.459586 1 405 303 304 m 5. 5.087596 1 406 303 304 f 0. 5.214936 1 407 305 306 m 8. 5.257495 1 408 305 306 f 7. 5.252273 1 410 312 311 f 1. 5.908083 1 411 314 313 m 1. 5.513429 1 414 330 329 m 2. 5.214936 ;;;; run echo echo ======== echo Test 138 echo ======== echo echo Variance Components analysis echo echo MENDEL WOMBAT (REML) echo Predictor Estimate ASE Estimate ASE echo --------------- -------- ------ -------- ------ echo Mean 5.4104 0.0683 echo Total variance 0.1074 echo Additive 0.0643 0.0283 0.067173 0.0314 echo Environmental 0.0431 0.0172 0.044411 0.0190 echo heritability 0.5990 0.1344 echo var logChol echo echo ======== echo Test 139 echo ======== echo mix logChol 2 echo echo Crude estimate increasing allele based on mixture model: 1-sqrt(0.6337) echo echo echo ======== echo Test 140 echo ======== echo set seeds 234 6324 24641 set burn 1000 set iter 1000 fpm logChol p a d fix d dval 1 echo echo MENDEL and PAP give: echo echo MLEs Genotypic Dominant echo 1/1 6.137 (0.129) 5.915 (0.0302) echo 1/2 5.885 (0.0325) 5.915 (0.0302) echo 2/2 5.333 (0.0204) 5.339 (0.0213) echo SD 0.153 (0.0122) 0.160 (0.0122) echo FREQ-1 0.071 (0.0411) 0.063 (0.0418) echo -2LL 1.5727 3.6453 echo