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

https://bitbucket.org/cistrome/cistrome-harvard/ · Plain Text · 128 lines · 118 code · 10 blank · 0 comment · 0 complexity · 01f3d6afa4e79e958d6042694f9d9738 MD5 · raw file 

    

  1. parameter file: rgEigPCAtest1_pca.xls.par
    2. 

  2. ### THE INPUT PARAMETERS
    3. 

  3. ##PARAMETER NAME: VALUE
    4. 

  4. genotypename: /opt/galaxy/test-data/tinywga.bed
    5. 

  5. snpname: /opt/galaxy/test-data/tinywga.bim
    6. 

  6. indivname: /opt/galaxy/test-data/tinywga.fam
    7. 

  7. evecoutname: rgEigPCAtest1_pca.xls.evec
    8. 

  8. evaloutname: rgEigPCAtest1_eval.xls
    9. 

  9. altnormstyle: NO
    10. 

  10. numoutevec: 4
    11. 

  11. numoutlieriter: 2
    12. 

  12. numoutlierevec: 2
    13. 

  13. outliersigmathresh: 2
    14. 

  14. qtmode: 0
    15. 

  15. ## smartpca version: 8000
    16. 

  16. norm used
    17. 

  17. 

  18. genetic distance set from physical distance
    19. 

  19. genotype file processed
    20. 

  20. number of samples used: 40 number of snps used: 25
    21. 

  21. REMOVED outlier 1334:2 iter 1 evec 1 sigmage -2.329
    22. 

  22. number of samples after outlier removal: 39
    23. 

  23. 

  24. ## Tracy-Widom statistics: rows: 39  cols: 24
    25. 

  25.   #N    eigenvalue  difference    twstat      p-value effect. n
    26. 

  26.    1     11.481974          NA    -0.712     0.332198     8.854
    27. 

  27.    2      7.739771   -3.742203    -1.302     0.510496     8.388
    28. 

  28.    3      7.254586   -0.485185    -0.171     0.201072     7.095
    29. 

  29.    4      4.270950   -2.983636    -0.191     0.205302     8.005
    30. 

  30.    5      2.538320   -1.732630    -0.341     0.238117     9.118
    31. 

  31.    6      1.667964   -0.870356    -0.231      0.21376     9.910
    32. 

  32.    7      1.043403   -0.624560    -0.269     0.222042    11.590
    33. 

  33.    8      0.653401   -0.390003        NA           NA        NA
    34. 

  34.    9      0.391044   -0.262357        NA           NA        NA
    35. 

  35.   10      0.338164   -0.052880        NA           NA        NA
    36. 

  36.   11      0.263384   -0.074780        NA           NA        NA
    37. 

  37.   12      0.150750   -0.112634        NA           NA        NA
    38. 

  38.   13      0.085580   -0.065170        NA           NA        NA
    39. 

  39.   14      0.065301   -0.020279        NA           NA        NA
    40. 

  40.   15      0.048797   -0.016504        NA           NA        NA
    41. 

  41.   16      0.006611   -0.042186        NA           NA        NA
    42. 

  42.     kurtosis           snps    indivs
    43. 

  43.  eigenvector    1     1.926     2.122
    44. 

  44.  eigenvector    2     2.599     2.148
    45. 

  45.  eigenvector    3     2.593     2.873
    46. 

  46.  eigenvector    4     3.165     2.831
    47. 

  47. population:   0                 Case    9
    48. 

  48. population:   1              Control   30
    49. 

  49. 

  50. ## Average divergence between populations:
    51. 

  51.                  Case    Control     popsize
    52. 

  52.       Case      1.028      0.954           9
    53. 

  53.    Control      0.954      0.972          30
    54. 

  54. 

  55. 

  56. number of blocks for moving block jackknife: 1
    57. 

  57. fst *1000:
    58. 

  58.           C     C 
    59. 

  59.    C      0     0
    60. 

  60.    C      0     0
    61. 

  61. 

  62. s.dev * 1000000:
    63. 

  63.           C     C 
    64. 

  64.    C      0     0
    65. 

  65.    C      0     0
    66. 

  66. 

  67. ## Anova statistics for population differences along each eigenvector:
    68. 

  68.                                               p-value
    69. 

  69.              eigenvector_1_Case_Control_      0.841067 
    70. 

  70.              eigenvector_2_Case_Control_      0.758376 
    71. 

  71.              eigenvector_3_Case_Control_      0.238793 
    72. 

  72.              eigenvector_4_Case_Control_      0.678458 
    73. 

  73. 

  74. ## Statistical significance of differences beween populations:
    75. 

  75.                                 pop1                  pop2      chisq          p-value   |pop1|   |pop2|
    76. 

  76. popdifference:                  Case               Control         1.810       0.77061       9      30
    77. 

  77. 

  78. eigbestsnp    1             rs762601 22     21898858     1.674
    79. 

  79. eigbestsnp    1            rs2156921 22     21899063     1.674
    80. 

  80. eigbestsnp    1            rs4822375 22     21905642     1.674
    81. 

  81. eigbestsnp    1            rs5751611 22     21896019     1.635
    82. 

  82. eigbestsnp    1            rs4820537 22     21794810     1.542
    83. 

  83. eigbestsnp    1            rs3788347 22     21797804     1.413
    84. 

  84. eigbestsnp    1            rs2267000 22     21785366     1.151
    85. 

  85. eigbestsnp    1            rs4820539 22     21807970     1.141
    86. 

  86. eigbestsnp    1            rs5751592 22     21827674     0.890
    87. 

  87. eigbestsnp    1            rs2283804 22     21820335     0.815
    88. 

  88. eigbestsnp    1            rs2267006 22     21820990     0.815
    89. 

  89. eigbestsnp    2            rs5759608 22     21832708     2.197
    90. 

  90. eigbestsnp    2            rs5759612 22     21833170     2.197
    91. 

  91. eigbestsnp    2            rs2283804 22     21820335     1.643
    92. 

  92. eigbestsnp    2            rs2267006 22     21820990     1.643
    93. 

  93. eigbestsnp    2            rs2283802 22     21784722     1.283
    94. 

  94. eigbestsnp    2            rs2267009 22     21860168     1.283
    95. 

  95. eigbestsnp    2            rs2071436 22     21871488     1.283
    96. 

  96. eigbestsnp    2             rs756632 22     21799918     0.942
    97. 

  97. eigbestsnp    2           rs16997606 22     21794754     0.715
    98. 

  98. eigbestsnp    2            rs6003566 22     21889806     0.645
    99. 

  99. eigbestsnp    2             rs762601 22     21898858     0.545
    100. 

  100. eigbestsnp    3           rs16997606 22     21794754     1.770
    101. 

  101. eigbestsnp    3            rs6003566 22     21889806     1.725
    102. 

  102. eigbestsnp    3            rs3788347 22     21797804     1.452
    103. 

  103. eigbestsnp    3            rs2267000 22     21785366     1.386
    104. 

  104. eigbestsnp    3            rs2283802 22     21784722     1.247
    105. 

  105. eigbestsnp    3            rs2267009 22     21860168     1.247
    106. 

  106. eigbestsnp    3            rs2071436 22     21871488     1.247
    107. 

  107. eigbestsnp    3            rs4820537 22     21794810     1.168
    108. 

  108. eigbestsnp    3             rs762601 22     21898858     1.153
    109. 

  109. eigbestsnp    3            rs2156921 22     21899063     1.153
    110. 

  110. eigbestsnp    3            rs4822375 22     21905642     1.153
    111. 

  111. eigbestsnp    4             rs756632 22     21799918     2.146
    112. 

  112. eigbestsnp    4            rs4820539 22     21807970     1.938
    113. 

  113. eigbestsnp    4            rs2267013 22     21875879     1.917
    114. 

  114. eigbestsnp    4            rs2256725 22     21892891     1.917
    115. 

  115. eigbestsnp    4            rs2283804 22     21820335     1.336
    116. 

  116. eigbestsnp    4            rs2267006 22     21820990     1.336
    117. 

  117. eigbestsnp    4            rs6003566 22     21889806     1.000
    118. 

  118. eigbestsnp    4           rs16997606 22     21794754     0.875
    119. 

  119. eigbestsnp    4            rs5751611 22     21896019     0.823
    120. 

  120. eigbestsnp    4            rs5759636 22     21868698     0.799
    121. 

  121. eigbestsnp    4            rs2267000 22     21785366     0.584
    122. 

  122. packedancestrymap output
    123. 

  123. ##end of smartpca run
    124. 

  124. 

  125. Correlation between eigenvector 1 (of 4) and Case/Control status is 0.033
    126. 

  126. Correlation between eigenvector 2 (of 4) and Case/Control status is 0.051
    127. 

  127. Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193
    128. 

  128. Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069
    129.