diff --git a/.gitignore b/.gitignore index b864d3c..3db6d4a 100644 --- a/.gitignore +++ b/.gitignore @@ -27,4 +27,3 @@ examples.qpGraph/*:log examples.qpGraph/*.ggg examples.qpGraph/*.dot examples.qpGraph/*.ps -examples/*.log 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/qp4diff.log b/examples/qp4diff.log new file mode 100644 index 0000000..4cd3b7a --- /dev/null +++ b/examples/qp4diff.log @@ -0,0 +1,23 @@ +parameter file: parqp4diff +### THE INPUT PARAMETERS +##PARAMETER NAME: VALUE +DIR: ../data/ +SSS: allmap +indivname: ../data//allmap.ind +snpname: ../data//allmap.snp +genotypename: ../data//allmap.geno +popfilename: list_qp4diff +## qp4diff version: 340 +packed geno read OK +end of inpack +nplist: 1 + 0 Yoruba 21 + 1 French 26 + 2 Han 32 + 3 Uygur 9 + 4 Japanese 28 +jackknife block size: 0.050 +snps: 621037 indivs: 116 +number of blocks for moving block jackknife: 711 +result: Yoruba French Han Uygur : Yoruba French Japanese Uygur 0.000088 0.000059 1.488 +##end of qp4diff: 17.700 seconds cpu 447.402 Mbytes in use diff --git a/examples/qpAdm.log b/examples/qpAdm.log new file mode 100644 index 0000000..0cc8ec8 --- /dev/null +++ b/examples/qpAdm.log @@ -0,0 +1,133 @@ +### lines added as comments by Nick +qpAdm: 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 +details: YES +## qpAdm version: 352 +packed geno read OK +end of inpack + +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: 0.764859564 dofdiff: 4 chisqdiff: -0.536 taildiff: 1 +### this is line for +B: + scale 1.000 1.000 + Eskimo 1.021 0.540 + Mbuti -0.990 1.738 + Karitiana 1.387 0.831 + Ulchi 0.233 0.001 +A: + scale 1205.754 3115.503 + WHG -0.476 -1.556 + LBK_EN -1.581 0.634 + Yamnaya 0.523 0.421 + + +full rank +f4info: +f4rank: 3 dof: 0 chisq: 0.000 tail: 1 dofdiff: 2 chisqdiff: 0.536 taildiff: 0.764859564 +### taildiff: is p-value for corank 1 against full rank (LRT). If very small qpAdm model is likely incorrect. +B: + scale 1.000 1.000 1.000 + Eskimo 0.988 0.490 1.642 + Mbuti -0.992 1.730 0.100 + Karitiana 1.409 0.875 -1.116 + Ulchi 0.231 -0.005 0.218 +A: + scale 1196.552 3119.151 29992.158 + WHG -0.492 -1.570 0.542 + LBK_EN -1.584 0.614 0.339 + Yamnaya 0.499 0.399 1.610 + + +best coefficients: 0.228 0.140 0.632 + +### CW = .228 WHG + .140 LBK_EN + .632 Yamnaya is best model +ssres: + 0.000046129 0.000008872 -0.000072290 0.000004983 + 1.068348230 0.205472447 -1.674245198 0.115395622 + +Jackknife mean: 0.224241123 0.142160839 0.633598038 + std. errors: 0.156 0.089 0.098 + +### std. errors are NOT independent + +error covariance (* 1000000) + 24258 -11342 -12916 + -11342 7951 3391 + -12916 3391 9526 + + + fixed pat wt dof chisq tail prob + 000 0 2 0.536 0.76486 0.228 0.140 0.632 + 001 1 3 14.811 0 1.291 -0.291 0.000 infeasible + 010 1 3 2.767 0.428944 0.436 0.000 0.564 + 100 1 3 2.710 0.438595 0.000 0.246 0.754 + 011 2 4 19.817 0.000542598 1.000 -0.000 0.000 + 101 2 4 168.302 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 0.438595 chi(nested): 2.173 p-value for nested model: 0.140407 +best pat: 011 0.000542598 chi(nested): 17.108 p-value for nested model: 3.53172e-05 + +## 100 (WHG dropped is fine model, but no model dropping 2 sources is much use. + +coeffs: 0.228 0.140 0.632 +details: WHG Eskimo -0.000623 -3.409522 +details: LBK_EN Eskimo -0.001193 -8.378403 +details: Yamnaya Eskimo 0.000563 4.139291 +dscore: Eskimo f4: 0.000046 Z: 0.364543 + +### Look at f4(CW, X; Han, Eskimo) where X is from leftpops. dscore is Z score for weighted sum (fitted model) + +details: WHG Mbuti -0.000461 -1.503609 +details: LBK_EN Mbuti 0.001655 7.167962 +details: Yamnaya Mbuti -0.000187 -0.814624 +dscore: Mbuti f4: 0.000009 Z: 0.042347 + +details: WHG Karitiana -0.001040 -3.869928 +details: LBK_EN Karitiana -0.001706 -8.173287 +details: Yamnaya Karitiana 0.000640 3.215214 +dscore: Karitiana f4: -0.000072 Z: -0.399554 + +details: WHG Ulchi -0.000088 -0.749233 +details: LBK_EN Ulchi -0.000304 -3.623063 +details: Yamnaya Ulchi 0.000107 1.230690 +dscore: Ulchi f4: 0.000005 Z: 0.064000 + +## 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