/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt
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1parameter file: rgEigPCAtest1_pca.xls.par 2### THE INPUT PARAMETERS 3##PARAMETER NAME: VALUE 4genotypename: /opt/galaxy/test-data/tinywga.bed 5snpname: /opt/galaxy/test-data/tinywga.bim 6indivname: /opt/galaxy/test-data/tinywga.fam 7evecoutname: rgEigPCAtest1_pca.xls.evec 8evaloutname: rgEigPCAtest1_eval.xls 9altnormstyle: NO 10numoutevec: 4 11numoutlieriter: 2 12numoutlierevec: 2 13outliersigmathresh: 2 14qtmode: 0 15## smartpca version: 8000 16norm used 17 18genetic distance set from physical distance 19genotype file processed 20number of samples used: 40 number of snps used: 25 21REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329 22number of samples after outlier removal: 39 23 24## Tracy-Widom statistics: rows: 39 cols: 24 25 #N eigenvalue difference twstat p-value effect. n 26 1 11.481974 NA -0.712 0.332198 8.854 27 2 7.739771 -3.742203 -1.302 0.510496 8.388 28 3 7.254586 -0.485185 -0.171 0.201072 7.095 29 4 4.270950 -2.983636 -0.191 0.205302 8.005 30 5 2.538320 -1.732630 -0.341 0.238117 9.118 31 6 1.667964 -0.870356 -0.231 0.21376 9.910 32 7 1.043403 -0.624560 -0.269 0.222042 11.590 33 8 0.653401 -0.390003 NA NA NA 34 9 0.391044 -0.262357 NA NA NA 35 10 0.338164 -0.052880 NA NA NA 36 11 0.263384 -0.074780 NA NA NA 37 12 0.150750 -0.112634 NA NA NA 38 13 0.085580 -0.065170 NA NA NA 39 14 0.065301 -0.020279 NA NA NA 40 15 0.048797 -0.016504 NA NA NA 41 16 0.006611 -0.042186 NA NA NA 42 kurtosis snps indivs 43 eigenvector 1 1.926 2.122 44 eigenvector 2 2.599 2.148 45 eigenvector 3 2.593 2.873 46 eigenvector 4 3.165 2.831 47population: 0 Case 9 48population: 1 Control 30 49 50## Average divergence between populations: 51 Case Control popsize 52 Case 1.028 0.954 9 53 Control 0.954 0.972 30 54 55 56number of blocks for moving block jackknife: 1 57fst *1000: 58 C C 59 C 0 0 60 C 0 0 61 62s.dev * 1000000: 63 C C 64 C 0 0 65 C 0 0 66 67## Anova statistics for population differences along each eigenvector: 68 p-value 69 eigenvector_1_Case_Control_ 0.841067 70 eigenvector_2_Case_Control_ 0.758376 71 eigenvector_3_Case_Control_ 0.238793 72 eigenvector_4_Case_Control_ 0.678458 73 74## Statistical significance of differences beween populations: 75 pop1 pop2 chisq p-value |pop1| |pop2| 76popdifference: Case Control 1.810 0.77061 9 30 77 78eigbestsnp 1 rs762601 22 21898858 1.674 79eigbestsnp 1 rs2156921 22 21899063 1.674 80eigbestsnp 1 rs4822375 22 21905642 1.674 81eigbestsnp 1 rs5751611 22 21896019 1.635 82eigbestsnp 1 rs4820537 22 21794810 1.542 83eigbestsnp 1 rs3788347 22 21797804 1.413 84eigbestsnp 1 rs2267000 22 21785366 1.151 85eigbestsnp 1 rs4820539 22 21807970 1.141 86eigbestsnp 1 rs5751592 22 21827674 0.890 87eigbestsnp 1 rs2283804 22 21820335 0.815 88eigbestsnp 1 rs2267006 22 21820990 0.815 89eigbestsnp 2 rs5759608 22 21832708 2.197 90eigbestsnp 2 rs5759612 22 21833170 2.197 91eigbestsnp 2 rs2283804 22 21820335 1.643 92eigbestsnp 2 rs2267006 22 21820990 1.643 93eigbestsnp 2 rs2283802 22 21784722 1.283 94eigbestsnp 2 rs2267009 22 21860168 1.283 95eigbestsnp 2 rs2071436 22 21871488 1.283 96eigbestsnp 2 rs756632 22 21799918 0.942 97eigbestsnp 2 rs16997606 22 21794754 0.715 98eigbestsnp 2 rs6003566 22 21889806 0.645 99eigbestsnp 2 rs762601 22 21898858 0.545 100eigbestsnp 3 rs16997606 22 21794754 1.770 101eigbestsnp 3 rs6003566 22 21889806 1.725 102eigbestsnp 3 rs3788347 22 21797804 1.452 103eigbestsnp 3 rs2267000 22 21785366 1.386 104eigbestsnp 3 rs2283802 22 21784722 1.247 105eigbestsnp 3 rs2267009 22 21860168 1.247 106eigbestsnp 3 rs2071436 22 21871488 1.247 107eigbestsnp 3 rs4820537 22 21794810 1.168 108eigbestsnp 3 rs762601 22 21898858 1.153 109eigbestsnp 3 rs2156921 22 21899063 1.153 110eigbestsnp 3 rs4822375 22 21905642 1.153 111eigbestsnp 4 rs756632 22 21799918 2.146 112eigbestsnp 4 rs4820539 22 21807970 1.938 113eigbestsnp 4 rs2267013 22 21875879 1.917 114eigbestsnp 4 rs2256725 22 21892891 1.917 115eigbestsnp 4 rs2283804 22 21820335 1.336 116eigbestsnp 4 rs2267006 22 21820990 1.336 117eigbestsnp 4 rs6003566 22 21889806 1.000 118eigbestsnp 4 rs16997606 22 21794754 0.875 119eigbestsnp 4 rs5751611 22 21896019 0.823 120eigbestsnp 4 rs5759636 22 21868698 0.799 121eigbestsnp 4 rs2267000 22 21785366 0.584 122packedancestrymap output 123##end of smartpca run 124 125Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033 126Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051 127Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 128Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069