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/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt

https://bitbucket.org/cistrome/cistrome-harvard/
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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