From adeae579566902271645ed4793cfefd154d0dfdf Mon Sep 17 00:00:00 2001 From: Mengyao Zhao Date: Fri, 8 Jan 2016 15:30:25 -0500 Subject: [PATCH] new example files are added --- examples/Rolloff.log | 60 ++++++ examples/Uygur | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:1 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:10 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:11 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:12 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:13 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:14 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:15 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:16 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:17 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:18 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:19 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:2 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:20 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:21 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:22 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:3 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:4 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:5 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:6 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:7 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:8 | 401 ++++++++++++++++++++++++++++++++++ examples/Uygur:9 | 401 ++++++++++++++++++++++++++++++++++ examples/elephant.ref | 2 + examples/elephant.target | 1 + examples/expfit.log | 10 + examples/expfit_Uygur.log | 442 ++++++++++++++++++++++++++++++++++++++ examples/qp3Pop.log | 22 ++ examples/qpAdm.log | 98 +++++++++ examples/qpBound.log | 20 ++ examples/qpDstat.log | 26 +++ examples/qpDstat1.log | 25 +++ examples/qpF4ratio.log | 25 +++ examples/qpWave.log | 84 ++++++++ examples/rolloff.par | 17 ++ examples/rolloff.ref | 2 + examples/rolloff.target | 1 + src/admixlib/nicklib.a | Bin 359972 -> 359972 bytes src/libnick.a | Bin 359972 -> 359972 bytes src/rolloff.c | 16 +- 41 files changed, 10067 insertions(+), 7 deletions(-) create mode 100644 examples/Rolloff.log create mode 100644 examples/Uygur create mode 100644 examples/Uygur:1 create mode 100644 examples/Uygur:10 create mode 100644 examples/Uygur:11 create mode 100644 examples/Uygur:12 create mode 100644 examples/Uygur:13 create mode 100644 examples/Uygur:14 create mode 100644 examples/Uygur:15 create mode 100644 examples/Uygur:16 create mode 100644 examples/Uygur:17 create mode 100644 examples/Uygur:18 create mode 100644 examples/Uygur:19 create mode 100644 examples/Uygur:2 create mode 100644 examples/Uygur:20 create mode 100644 examples/Uygur:21 create mode 100644 examples/Uygur:22 create mode 100644 examples/Uygur:3 create mode 100644 examples/Uygur:4 create mode 100644 examples/Uygur:5 create mode 100644 examples/Uygur:6 create mode 100644 examples/Uygur:7 create mode 100644 examples/Uygur:8 create mode 100644 examples/Uygur:9 create mode 100644 examples/elephant.ref create mode 100644 examples/elephant.target create mode 100644 examples/expfit.log create mode 100644 examples/expfit_Uygur.log create mode 100644 examples/qp3Pop.log create mode 100644 examples/qpAdm.log create mode 100644 examples/qpBound.log create mode 100644 examples/qpDstat.log create mode 100644 examples/qpDstat1.log create mode 100644 examples/qpF4ratio.log create mode 100644 examples/qpWave.log create mode 100644 examples/rolloff.par create mode 100644 examples/rolloff.ref create mode 100644 examples/rolloff.target diff --git a/examples/Rolloff.log b/examples/Rolloff.log new file mode 100644 index 0000000..d99c67c --- /dev/null +++ b/examples/Rolloff.log @@ -0,0 +1,60 @@ +Sender: LSF System +Subject: Job 246984: <../bin/rolloff -p parRolloff> Done + +Job <../bin/rolloff -p parRolloff> was submitted from host by user in cluster . +Job was executed on host(s) , in queue , as user in cluster . + was used as the home directory. + was used as the working directory. +Started at Sun Sep 9 02:44:53 2012 +Results reported at Sun Sep 9 14:16:35 2012 + +Your job looked like: + +------------------------------------------------------------ +# LSBATCH: User input +../bin/rolloff -p parRolloff +------------------------------------------------------------ + +Successfully completed. + +Resource usage summary: + + CPU time : 41447.75 sec. + Max Memory : 437 MB + Max Swap : 474 MB + + Max Processes : 3 + Max Threads : 4 + +The output (if any) follows: + + +## rolloff. Version 1000 + +parameter file: parRolloff +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +poplistname: rolloff.ref +admixlist: rolloff.target +binsize: .001 +output: Uygur +maxdis: 0.4 +seed: 77 +runmode: 1 +mincount: 4 +minparentcount: 0 +jackknife: YES +seed: 77 +chithresh: 6.000 +genotypename: ../data//allmap.geno +packed geno read OK +valid snps: 621038 +group 0 French +group 1 Han +number admixed: 9 number of references: 2 +numsnps: 621038 numindivs: 67 +starting main loop. numsnps: 465168 +##end of run diff --git a/examples/Uygur b/examples/Uygur new file mode 100644 index 0000000..431dd3a --- /dev/null +++ b/examples/Uygur @@ -0,0 +1,401 @@ + ##Z-score and correlation:: elephant.ref binsize: 0.001000 + 0.100 0.000000 0.000000 0.000000 0 + 0.200 0.000000 0.000000 0.000000 0 + 0.300 0.000000 0.000000 0.000000 0 + 0.400 0.000000 0.000000 0.000000 0 + 0.500 0.000000 0.000000 0.000000 0 + 0.600 0.000000 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/dev/null +++ b/examples/elephant.ref @@ -0,0 +1,2 @@ +L_cyc +M_pri diff --git a/examples/elephant.target b/examples/elephant.target new file mode 100644 index 0000000..2132c08 --- /dev/null +++ b/examples/elephant.target @@ -0,0 +1 @@ +M_col diff --git a/examples/expfit.log b/examples/expfit.log new file mode 100644 index 0000000..919fb61 --- /dev/null +++ b/examples/expfit.log @@ -0,0 +1,10 @@ +Running rexpfit.r +Input file: Uygur +Output file: expfit_Uygur +Expfit logfile: expfit_Uygur.flog +Output plot: expfit_Uygur.pdf +Jackknife logfile: expfit_Uygur.log + +Jackknife summary: Uygur.jin +Jackknife mean: 22.557 +Jackknife std. err: 2.498 diff --git a/examples/expfit_Uygur.log b/examples/expfit_Uygur.log new file mode 100644 index 0000000..8d084fd --- /dev/null +++ b/examples/expfit_Uygur.log @@ -0,0 +1,442 @@ +Jackknife Results: + + +Input file Uygur:1 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.417e-03 4.363e-04 14.71 <2e-16 *** +A 9.500e-02 2.369e-03 40.10 <2e-16 *** +m 2.243e+01 8.458e-01 26.52 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006444 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 2.211e-06 + +mean (generations): 22.43102 + +Input file Uygur:2 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.234e-03 4.555e-04 13.69 <2e-16 *** +A 9.726e-02 2.547e-03 38.19 <2e-16 *** +m 2.304e+01 9.037e-01 25.49 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006798 on 393 degrees of freedom + +Number of iterations to convergence: 0 +Achieved convergence tolerance: 3.3e-06 + +mean (generations): 23.03956 + +Input file Uygur:3 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.118e-03 4.463e-04 13.71 <2e-16 *** +A 9.495e-02 2.534e-03 37.46 <2e-16 *** +m 2.338e+01 9.301e-01 25.13 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006697 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 2.662e-06 + +mean (generations): 23.375217 + +Input file Uygur:4 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.470e-03 4.542e-04 14.24 <2e-16 *** +A 9.631e-02 2.470e-03 38.99 <2e-16 *** +m 2.246e+01 8.707e-01 25.80 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006713 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 7.072e-07 + +mean (generations): 22.463408 + +Input file Uygur:5 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 5.764e-03 4.723e-04 12.20 <2e-16 *** +A 9.649e-02 2.494e-03 38.69 <2e-16 *** +m 2.188e+01 8.627e-01 25.36 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006905 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 1.58e-06 + +mean (generations): 21.875488 + +Input file Uygur:6 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.322e-03 4.468e-04 14.15 <2e-16 *** +A 9.656e-02 2.410e-03 40.07 <2e-16 *** +m 2.229e+01 8.431e-01 26.44 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006583 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 3.786e-06 + +mean (generations): 22.294106 + +Input file Uygur:7 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.269e-03 4.647e-04 13.49 <2e-16 *** +A 9.606e-02 2.593e-03 37.04 <2e-16 *** +m 2.300e+01 9.307e-01 24.71 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006931 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 4.336e-06 + +mean (generations): 23.00005 + +Input file Uygur:8 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 5.879e-03 4.717e-04 12.46 <2e-16 *** +A 9.408e-02 2.413e-03 38.99 <2e-16 *** +m 2.126e+01 8.409e-01 25.29 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006814 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 6.763e-06 + +mean (generations): 21.263476 + +Input file Uygur:9 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.745e-03 4.541e-04 14.85 <2e-16 *** +A 9.687e-02 2.565e-03 37.77 <2e-16 *** +m 2.326e+01 9.193e-01 25.30 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006801 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 7.083e-06 + +mean (generations): 23.255262 + +Input file Uygur:10 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.182e-03 4.678e-04 13.21 <2e-16 *** +A 9.572e-02 2.606e-03 36.73 <2e-16 *** +m 2.296e+01 9.375e-01 24.49 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006973 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 6.047e-06 + +mean (generations): 22.961465 + +Input file Uygur:11 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 5.521e-03 4.799e-04 11.5 <2e-16 *** +A 9.633e-02 2.582e-03 37.3 <2e-16 *** +m 2.225e+01 9.044e-01 24.6 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.007065 on 393 degrees of freedom + +Number of iterations to convergence: 2 +Achieved convergence tolerance: 5.356e-06 + +mean (generations): 22.248003 + +Input file Uygur:12 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.265e-03 4.504e-04 13.91 <2e-16 *** +A 9.762e-02 2.539e-03 38.45 <2e-16 *** +m 2.322e+01 9.021e-01 25.73 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006741 on 393 degrees of freedom + +Number of iterations to convergence: 0 +Achieved convergence tolerance: 9.571e-06 + +mean (generations): 23.215761 + +Input file Uygur:13 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.127e-03 4.535e-04 13.51 <2e-16 *** +A 9.660e-02 2.509e-03 38.50 <2e-16 *** +m 2.282e+01 8.909e-01 25.61 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006744 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 3.174e-06 + +mean (generations): 22.820432 + +Input file Uygur:14 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 5.910e-03 4.597e-04 12.86 <2e-16 *** +A 9.564e-02 2.444e-03 39.13 <2e-16 *** +m 2.201e+01 8.561e-01 25.71 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006738 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 4.913e-06 + +mean (generations): 22.006584 + +Input file Uygur:15 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 5.655e-03 4.557e-04 12.41 <2e-16 *** +A 9.489e-02 2.481e-03 38.24 <2e-16 *** +m 2.249e+01 8.883e-01 25.32 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006738 on 393 degrees of freedom + +Number of iterations to convergence: 2 +Achieved convergence tolerance: 7.342e-06 + +mean (generations): 22.486762 + +Input file Uygur:16 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.054e-03 4.438e-04 13.64 <2e-16 *** +A 9.711e-02 2.504e-03 38.78 <2e-16 *** +m 2.323e+01 8.949e-01 25.96 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006645 on 393 degrees of freedom + +Number of iterations to convergence: 2 +Achieved convergence tolerance: 4.736e-06 + +mean (generations): 23.232993 + +Input file Uygur:17 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.662e-03 4.474e-04 14.89 <2e-16 *** +A 9.573e-02 2.496e-03 38.35 <2e-16 *** +m 2.299e+01 8.986e-01 25.59 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006672 on 393 degrees of freedom + +Number of iterations to convergence: 0 +Achieved convergence tolerance: 8.211e-06 + +mean (generations): 22.993169 + +Input file Uygur:18 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.083e-03 4.546e-04 13.38 <2e-16 *** +A 9.629e-02 2.515e-03 38.29 <2e-16 *** +m 2.282e+01 8.957e-01 25.48 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006759 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 3.398e-06 + +mean (generations): 22.818852 + +Input file Uygur:19 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.455e-03 4.434e-04 14.56 <2e-16 *** +A 9.687e-02 2.503e-03 38.70 <2e-16 *** +m 2.324e+01 8.969e-01 25.92 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.00664 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 1.565e-06 + +mean (generations): 23.243286 + +Input file Uygur:20 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.507e-03 4.434e-04 14.68 <2e-16 *** +A 9.658e-02 2.468e-03 39.14 <2e-16 *** +m 2.294e+01 8.793e-01 26.09 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006607 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 5.023e-07 + +mean (generations): 22.941403 + +Input file Uygur:21 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.162e-03 4.549e-04 13.55 <2e-16 *** +A 9.531e-02 2.461e-03 38.72 <2e-16 *** +m 2.236e+01 8.741e-01 25.58 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.00671 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 1.059e-08 + +mean (generations): 22.36003 + +Input file Uygur:22 +Summary of fit: + +Formula: wcorr ~ (C + A * exp(-m * dist/100)) + +Parameters: + Estimate Std. Error t value Pr(>|t|) +C 6.309e-03 4.489e-04 14.05 <2e-16 *** +A 9.545e-02 2.440e-03 39.12 <2e-16 *** +m 2.245e+01 8.675e-01 25.88 <2e-16 *** +--- +Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 + +Residual standard error: 0.006633 on 393 degrees of freedom + +Number of iterations to convergence: 1 +Achieved convergence tolerance: 2.337e-06 + +mean (generations): 22.45368 diff --git a/examples/qp3Pop.log b/examples/qp3Pop.log new file mode 100644 index 0000000..2b1242d --- /dev/null +++ b/examples/qp3Pop.log @@ -0,0 +1,22 @@ +parameter file: parqp3Pop +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +popfilename: list_qp3Pop +## qp3Pop version: 300 +packed geno read OK +nplist: 6 +number of blocks for block jackknife: 711 +snps: 621038 + Source 1 Source 2 Target f_3 std. err Z SNPs + result: French Japanese Uygur -0.025170 0.000379 -66.384 428873 + result: French Han Uygur -0.025172 0.000375 -67.090 429972 + result: Russian Japanese Uygur -0.021377 0.000357 -59.897 428523 + result: Russian Han Uygur -0.021403 0.000363 -58.920 429573 + result: Italian Japanese Uygur -0.025345 0.000391 -64.880 424716 + result: Italian Han Uygur -0.025102 0.000400 -62.757 425595 +##end of qp3Pop diff --git a/examples/qpAdm.log b/examples/qpAdm.log new file mode 100644 index 0000000..d31cbf1 --- /dev/null +++ b/examples/qpAdm.log @@ -0,0 +1,98 @@ +parameter file: parqpAdm +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data +S1: qpdata +indivname: ../data/qpdata.ind +snpname: ../data/qpdata.snp +genotypename: ../data/qpdata.geno +popleft: left1 +popright: right1 +## qpAdm version: 103 + +left pops: +Corded_Ware_LN +WHG +LBK_EN +Yamnaya + +right pops: +Han +Eskimo +Mbuti +Karitiana +Ulchi + + 0 Corded_Ware_LN 4 + 1 WHG 2 + 2 LBK_EN 12 + 3 Yamnaya 9 + 4 Han 33 + 5 Eskimo 22 + 6 Mbuti 10 + 7 Karitiana 12 + 8 Ulchi 25 +jackknife block size: 0.050 +snps: 354212 indivs: 129 +number of blocks for block jackknife: 710 +dof (jackknife): 606.426 +numsnps used: 351683 +codimension 1 +f4info: +f4rank: 2 dof: 2 chisq: 0.536 tail: 0.764859692 dofdiff: 4 chisqdiff: -0.536 taildiff: 1 +B: + scale 1.000 1.000 + Eskimo 1.021 0.540 + Mbuti -0.990 1.738 + Karitiana 1.387 0.830 + Ulchi 0.233 0.001 +A: + scale 1202.997 3105.760 + WHG -0.477 -1.556 + LBK_EN -1.581 0.634 + Yamnaya 0.522 0.420 + + +full rank 1 +f4info: +f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 2 chisqdiff: 0.536 taildiff: 0.764859692 +B: + scale 1.000 1.000 1.000 + Eskimo 0.988 0.490 1.642 + Mbuti -0.992 1.730 0.101 + Karitiana 1.409 0.875 -1.116 + Ulchi 0.231 -0.005 0.218 +A: + scale 1193.784 3109.317 29979.194 + WHG -0.493 -1.570 0.541 + LBK_EN -1.584 0.614 0.338 + Yamnaya 0.498 0.398 1.610 + + +best coefficients: 0.228 0.140 0.632 +ssres: + 0.000046181 0.000008882 -0.000072372 0.000004988 + 1.068346751 0.205479302 -1.674245163 0.115397621 + +Jackknife mean: 0.223656191 0.141994680 0.634349129 + std. errors: 0.155 0.089 0.097 + +error covariance (* 1000000) + 24169 -11297 -12872 + -11297 7925 3372 + -12872 3372 9500 + + + fixed pat wt dof chisq tail prob + 000 0 2 0.536 0.76486 0.228 0.140 0.632 + 001 1 3 14.812 0 1.292 -0.292 0.000 infeasible + 010 1 3 2.767 0.42894 0.435 0.000 0.565 + 100 1 3 2.710 0.438597 0.000 0.245 0.755 + 011 2 4 19.818 0.000542525 1.000 -0.000 0.000 + 101 2 4 168.305 0 0.000 1.000 0.000 + 110 2 4 22.430 0.000164556 0.000 -0.000 1.000 +best pat: 000 0.76486 - - +best pat: 100 0.438597 chi(nested): 2.173 p-value for nested model: 0.140408 +best pat: 011 0.000542525 chi(nested): 17.108 p-value for nested model: 3.53115e-05 + +## end of run diff --git a/examples/qpBound.log b/examples/qpBound.log new file mode 100644 index 0000000..bd3c52c --- /dev/null +++ b/examples/qpBound.log @@ -0,0 +1,20 @@ +parameter file: parqpBound +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +popfilename: list_qpBound +outpop: Yoruba +## qpBound version: 120 +packed geno read OK +nplist: 6 + French Japanese Uygur -0.025170 -66.384 0.447 0.531 + French Han Uygur -0.025172 -67.090 0.437 0.527 +Russian Japanese Uygur -0.021377 -59.897 0.544 0.587 +Russian Han Uygur -0.021403 -58.920 0.533 0.583 +Italian Japanese Uygur -0.025345 -64.880 0.422 0.521 +Italian Han Uygur -0.025102 -62.757 0.411 0.520 +##end of qpBound diff --git a/examples/qpDstat.log b/examples/qpDstat.log new file mode 100644 index 0000000..43e2249 --- /dev/null +++ b/examples/qpDstat.log @@ -0,0 +1,26 @@ +parameter file: parqpDstat +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +poplistname: list_qpDstat +## qpDstat version: 662 +packed geno read OK + 0 Yoruba 21 + 1 French 26 + 2 Han 32 + 3 Uygur 9 +jackknife block size: 0.050 +nodata: Affx-50079445 +nodata: Affx-36048139 +nodata: Affx-50056055 +snps: 621035 indivs: 88 +number of blocks for jackknife: 711 +nrows, ncols: 88 621035 +result: Yoruba French Han Uygur 0.0410 32.300 - 30753 28328 621026 +result: Yoruba Han French Uygur 0.0865 51.447 - 33690 28328 621026 +result: Yoruba Uygur French Han 0.0456 22.403 best 33690 30753 621026 +## end of run diff --git a/examples/qpDstat1.log b/examples/qpDstat1.log new file mode 100644 index 0000000..6c9195c --- /dev/null +++ b/examples/qpDstat1.log @@ -0,0 +1,25 @@ +parameter file: parqpDstat1 +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +popfilename: list_qpDstat1 +## qpDstat version: 662 +packed geno read OK +number of quadruples 2 + 0 Yoruba 21 + 1 French 26 + 2 Han 32 + 3 Japanese 28 + 4 Uygur 9 +jackknife block size: 0.050 +nodata: Affx-50079445 +snps: 621037 indivs: 116 +number of blocks for jackknife: 711 +nrows, ncols: 116 621037 +result: Yoruba French Han Uygur 0.0410 32.300 30753 28328 621026 +result: Yoruba French Japanese Uygur 0.0402 31.016 30690 28320 621026 +## end of run diff --git a/examples/qpF4ratio.log b/examples/qpF4ratio.log new file mode 100644 index 0000000..063174f --- /dev/null +++ b/examples/qpF4ratio.log @@ -0,0 +1,25 @@ +parameter file: parqpF4ratio +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +popfilename: list_qpF4ratio +## qpF4ratio version: 300 +packed geno read OK +nplist: 2 + 0 Yoruba 21 + 1 Papuan 12 + 2 Uygur 9 + 3 Han 32 + 4 French 26 + 5 Adygei 15 +jackknife block size: 0.050 +snps: 621038 indivs: 115 +number of blocks for block jackknife: 711 + alpha std. err Z (null=0) + result: Yoruba Papuan Uygur Han : Yoruba Papuan French Han 0.467437 0.015800 29.585 + result: Yoruba Adygei Uygur Han : Yoruba Adygei French Han 0.474091 0.011546 41.060 +## end of run diff --git a/examples/qpWave.log b/examples/qpWave.log new file mode 100644 index 0000000..e05bed5 --- /dev/null +++ b/examples/qpWave.log @@ -0,0 +1,84 @@ +parameter file: parqpWave +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data +S1: qpdata +indivname: ../data/qpdata.ind +snpname: ../data/qpdata.snp +genotypename: ../data/qpdata.geno +popleft: left1 +popright: right1 +## qpWave version: 201 + +left pops: +Corded_Ware_LN +WHG +LBK_EN +Yamnaya + +right pops: +Han +Eskimo +Mbuti +Karitiana +Ulchi + 0 Corded_Ware_LN 4 + 1 WHG 2 + 2 LBK_EN 12 + 3 Yamnaya 9 + 4 Han 33 + 5 Eskimo 22 + 6 Mbuti 10 + 7 Karitiana 12 + 8 Ulchi 25 +jackknife block size: 0.050 +snps: 354212 indivs: 129 +number of blocks for block jackknife: 710 +dof (jackknife): 606.426 +numsnps used: 351683 +f4info: +f4rank: 0 dof: 12 chisq: 460.444 tail: 5.71351953e-91 dofdiff: 0 chisqdiff: 0.000 taildiff: 1 + +f4info: +f4rank: 1 dof: 6 chisq: 24.489 tail: 0.00042443713 dofdiff: 6 chisqdiff: 435.955 taildiff: 5.16806732e-91 +B: + scale 1.000 + Eskimo 0.966 + Mbuti -1.099 + Karitiana 1.342 + Ulchi 0.246 +A: + scale 1211.444 + WHG -0.427 + LBK_EN -1.594 + Yamnaya 0.525 + +f4info: +f4rank: 2 dof: 2 chisq: 0.536 tail: 0.764859692 dofdiff: 4 chisqdiff: 23.953 taildiff: 8.16355044e-05 +B: + scale 1.000 1.000 + Eskimo 1.021 0.540 + Mbuti -0.990 1.738 + Karitiana 1.387 0.830 + Ulchi 0.233 0.001 +A: + scale 1202.997 3105.760 + WHG -0.477 -1.556 + LBK_EN -1.581 0.634 + Yamnaya 0.522 0.420 + +f4info: +f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 2 chisqdiff: 0.536 taildiff: 0.764859692 +B: + scale 1.000 1.000 1.000 + Eskimo 0.988 0.490 1.642 + Mbuti -0.992 1.730 0.101 + Karitiana 1.409 0.875 -1.116 + Ulchi 0.231 -0.005 0.218 +A: + scale 1193.784 3109.317 29979.194 + WHG -0.493 -1.570 0.541 + LBK_EN -1.584 0.614 0.338 + Yamnaya 0.498 0.398 1.610 + +## end of run diff --git a/examples/rolloff.par b/examples/rolloff.par new file mode 100644 index 0000000..312ef60 --- /dev/null +++ b/examples/rolloff.par @@ -0,0 +1,17 @@ +DIR: /groups/reich/eleftheria/AdmixTools/ +indivname: DIR/majfas_mindepth_3_compiled_0.1_eigenstrat.ind +snpname: DIR/majfas_mindepth_3_compiled_0.1_eigenstrat_mod.snp +genotypename: DIR/majfas_mindepth_3_compiled_0.1_eigenstrat.geno +poplistname: elephant.ref +admixlist: elephant.target +binsize: .001 +output: Uygur +maxdis: 0.4 +seed: 77 +runmode: 1 +mincount: 4 +minparentcount: 0 +jackknife: YES +chithresh: 6.000 +numchrom: 28 +checkmap: NO diff --git a/examples/rolloff.ref b/examples/rolloff.ref new file mode 100644 index 0000000..f59e42b --- /dev/null +++ b/examples/rolloff.ref @@ -0,0 +1,2 @@ +French +Han diff --git a/examples/rolloff.target b/examples/rolloff.target new file mode 100644 index 0000000..ed22d20 --- /dev/null +++ b/examples/rolloff.target @@ -0,0 +1 @@ +Uygur diff --git a/src/admixlib/nicklib.a b/src/admixlib/nicklib.a index 77fdb2d8c367dbbc4e5b69254ee6ce1e6f55455d..47afe0dae592d16255b450bd86cd5f2105e29705 100644 GIT binary patch delta 35 qcmZ4TM|8;_(Fs!QrbdRAMux_Ximi%_t%^*oip;HwEL#;>nd<=6DheY2 delta 31 ncmZ4TM|8;_(Fs!1qkge)HLA3#Ft(~NwW=_;s<13oVXXrI%L59n diff --git a/src/libnick.a b/src/libnick.a index 77fdb2d8c367dbbc4e5b69254ee6ce1e6f55455d..47afe0dae592d16255b450bd86cd5f2105e29705 100644 GIT binary patch delta 35 qcmZ4TM|8;_(Fs!QrbdRAMux_Ximi%_t%^*oip;HwEL#;>nd<=6DheY2 delta 31 ncmZ4TM|8;_(Fs!1qkge)HLA3#Ft(~NwW=_;s<13oVXXrI%L59n diff --git a/src/rolloff.c b/src/rolloff.c index 32f50c5..56816df 100644 --- a/src/rolloff.c +++ b/src/rolloff.c @@ -18,7 +18,7 @@ #include "egsubs.h" #include "ldsubs.h" -#define WVERSION "1002" +#define WVERSION "1100" /** an attempt to 1) threshold for LD in parentals 2) Use a weighted Z-score @@ -29,13 +29,14 @@ nochrom added zdipmode added mincount default now 5 - Jackknife output for 22 autosomes + Jackknife output for numchrom autosomes Bug in clearcorr fixed Bug in dumpit callfixed xnochrom added checkmap added (default) First admixtools release Count of outer + inner loop made + numchrom parametric */ @@ -265,7 +266,7 @@ int main(int argc, char **argv) chrom = cupt -> chrom ; if (chrom<1) cupt -> ignore = YES ; - if (chrom>22) cupt -> ignore = YES ; + if (chrom>numchrom) cupt -> ignore = YES ; if ((xchrom>0) && (chrom != xchrom)) cupt -> ignore = YES ; if (chrom == xnochrom) cupt -> ignore = YES ; if (cupt -> ignore == NO) ++t ; @@ -836,6 +837,7 @@ int readcommands(int argc, char **argv) getint(ph, "flatmode:", &flatmode) ; getint(ph, "zdipcorrmode:", &zdipcorrmode) ; getint(ph, "jackknife:", &jackknife) ; + getint(ph, "numchrom:", &numchrom) ; getdbl(ph, "maxdis:", &maxdis) ; getdbl(ph, "binsize:", &binsize) ; @@ -867,7 +869,7 @@ void setfc(SNP **snpm, int numsnps) // if (cupt -> isfake) continue ; if (cupt -> ignore) continue ; chrom = cupt -> chrom ; -// if ((noxdata) && (chrom==23)) continue ; +// if ((noxdata) && (chrom==(numchrom+1))) continue ; fchrom[chrom] = MIN(fchrom[chrom],i) ; lchrom[chrom] = MAX(lchrom[chrom],i) ; } @@ -921,7 +923,7 @@ double cntit1(double *xc, SNP *cupt, Indiv **indm, int numindivs, int t) int k, g ; vzero(xc, 3) ; - if (cupt -> ignore) return 0; + if (cupt -> ignore) return ; for (k=0; k ignore) continue ; @@ -940,8 +942,8 @@ double cntit2(double *xc, SNP *cupt, SNP *cupt2, Indiv **indm, int numindivs, in int k, e, f ; vzero(xc, 9) ; - if (cupt -> ignore) return 0; - if (cupt2 -> ignore) return 0; + if (cupt -> ignore) return ; + if (cupt2 -> ignore) return ; for (k=0; k ignore) continue ;