This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 6 clinical features across 553 patients, 11 significant findings detected with Q value < 0.25.
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7P GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
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7Q GAIN MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
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10P GAIN MUTATION ANALYSIS cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
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20P GAIN MUTATION ANALYSIS cnv correlated to 'AGE'.
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20Q GAIN MUTATION ANALYSIS cnv correlated to 'AGE'.
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10P LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
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10Q LOSS MUTATION ANALYSIS cnv correlated to 'Time to Death' and 'AGE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | |
7P GAIN MUTATION ANALYSIS | 447 (81%) | 106 |
9.19e-05 (0.0434) |
3.03e-06 (0.00144) |
0.912 (1.00) |
0.389 (1.00) |
0.0116 (1.00) |
0.199 (1.00) |
7Q GAIN MUTATION ANALYSIS | 451 (82%) | 102 |
0.000228 (0.108) |
1.38e-05 (0.00657) |
0.575 (1.00) |
0.547 (1.00) |
0.00923 (1.00) |
0.235 (1.00) |
10P LOSS MUTATION ANALYSIS | 460 (83%) | 93 |
9.78e-06 (0.00465) |
6.53e-08 (3.13e-05) |
0.163 (1.00) |
0.166 (1.00) |
0.00128 (0.597) |
0.713 (1.00) |
10Q LOSS MUTATION ANALYSIS | 472 (85%) | 81 |
6.88e-05 (0.0326) |
1.16e-06 (0.000553) |
0.462 (1.00) |
0.0059 (1.00) |
0.0202 (1.00) |
0.796 (1.00) |
10P GAIN MUTATION ANALYSIS | 12 (2%) | 541 |
0.00435 (1.00) |
0.0026 (1.00) |
0.0712 (1.00) |
0.00032 (0.15) |
0.467 (1.00) |
1 (1.00) |
20P GAIN MUTATION ANALYSIS | 209 (38%) | 344 |
0.808 (1.00) |
5.28e-05 (0.025) |
0.325 (1.00) |
0.434 (1.00) |
0.469 (1.00) |
0.636 (1.00) |
20Q GAIN MUTATION ANALYSIS | 207 (37%) | 346 |
0.898 (1.00) |
0.000249 (0.117) |
0.281 (1.00) |
0.563 (1.00) |
0.468 (1.00) |
0.635 (1.00) |
1P GAIN MUTATION ANALYSIS | 75 (14%) | 478 |
0.0625 (1.00) |
0.8 (1.00) |
0.446 (1.00) |
0.391 (1.00) |
0.385 (1.00) |
0.594 (1.00) |
1Q GAIN MUTATION ANALYSIS | 82 (15%) | 471 |
0.228 (1.00) |
0.994 (1.00) |
0.272 (1.00) |
0.434 (1.00) |
0.567 (1.00) |
0.606 (1.00) |
2P GAIN MUTATION ANALYSIS | 32 (6%) | 521 |
0.833 (1.00) |
0.766 (1.00) |
0.061 (1.00) |
0.941 (1.00) |
0.609 (1.00) |
0.695 (1.00) |
2Q GAIN MUTATION ANALYSIS | 30 (5%) | 523 |
0.838 (1.00) |
0.834 (1.00) |
0.251 (1.00) |
0.693 (1.00) |
0.579 (1.00) |
1 (1.00) |
3P GAIN MUTATION ANALYSIS | 52 (9%) | 501 |
0.983 (1.00) |
0.0421 (1.00) |
0.183 (1.00) |
0.176 (1.00) |
0.876 (1.00) |
1 (1.00) |
3Q GAIN MUTATION ANALYSIS | 58 (10%) | 495 |
0.736 (1.00) |
0.171 (1.00) |
0.258 (1.00) |
0.151 (1.00) |
0.679 (1.00) |
0.653 (1.00) |
4P GAIN MUTATION ANALYSIS | 34 (6%) | 519 |
0.704 (1.00) |
0.0943 (1.00) |
1 (1.00) |
0.0763 (1.00) |
1 (1.00) |
0.25 (1.00) |
4Q GAIN MUTATION ANALYSIS | 32 (6%) | 521 |
0.399 (1.00) |
0.242 (1.00) |
0.71 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.0742 (1.00) |
5P GAIN MUTATION ANALYSIS | 45 (8%) | 508 |
0.957 (1.00) |
0.352 (1.00) |
0.111 (1.00) |
0.0432 (1.00) |
0.0714 (1.00) |
0.867 (1.00) |
5Q GAIN MUTATION ANALYSIS | 38 (7%) | 515 |
0.844 (1.00) |
0.64 (1.00) |
0.0571 (1.00) |
0.275 (1.00) |
0.124 (1.00) |
1 (1.00) |
6P GAIN MUTATION ANALYSIS | 22 (4%) | 531 |
0.627 (1.00) |
0.523 (1.00) |
0.512 (1.00) |
0.543 (1.00) |
1 (1.00) |
0.242 (1.00) |
6Q GAIN MUTATION ANALYSIS | 21 (4%) | 532 |
0.556 (1.00) |
0.269 (1.00) |
1 (1.00) |
0.489 (1.00) |
1 (1.00) |
0.632 (1.00) |
8P GAIN MUTATION ANALYSIS | 47 (8%) | 506 |
0.735 (1.00) |
0.277 (1.00) |
0.28 (1.00) |
0.895 (1.00) |
0.731 (1.00) |
0.624 (1.00) |
8Q GAIN MUTATION ANALYSIS | 53 (10%) | 500 |
0.636 (1.00) |
0.0985 (1.00) |
0.239 (1.00) |
0.791 (1.00) |
0.766 (1.00) |
0.876 (1.00) |
9P GAIN MUTATION ANALYSIS | 45 (8%) | 508 |
0.543 (1.00) |
0.505 (1.00) |
0.0559 (1.00) |
0.724 (1.00) |
0.504 (1.00) |
0.738 (1.00) |
9Q GAIN MUTATION ANALYSIS | 70 (13%) | 483 |
0.706 (1.00) |
0.488 (1.00) |
0.0664 (1.00) |
0.549 (1.00) |
0.724 (1.00) |
0.681 (1.00) |
10Q GAIN MUTATION ANALYSIS | 3 (1%) | 550 |
0.454 (1.00) |
0.907 (1.00) |
0.565 (1.00) |
1 (1.00) |
0.227 (1.00) |
|
11P GAIN MUTATION ANALYSIS | 13 (2%) | 540 |
0.326 (1.00) |
0.246 (1.00) |
0.775 (1.00) |
0.501 (1.00) |
1 (1.00) |
0.763 (1.00) |
11Q GAIN MUTATION ANALYSIS | 13 (2%) | 540 |
0.118 (1.00) |
0.0383 (1.00) |
0.264 (1.00) |
0.0793 (1.00) |
0.495 (1.00) |
0.362 (1.00) |
12P GAIN MUTATION ANALYSIS | 56 (10%) | 497 |
0.667 (1.00) |
0.219 (1.00) |
0.666 (1.00) |
0.57 (1.00) |
1 (1.00) |
0.762 (1.00) |
12Q GAIN MUTATION ANALYSIS | 45 (8%) | 508 |
0.952 (1.00) |
0.644 (1.00) |
0.34 (1.00) |
0.879 (1.00) |
0.416 (1.00) |
0.867 (1.00) |
13Q GAIN MUTATION ANALYSIS | 11 (2%) | 542 |
0.606 (1.00) |
0.0472 (1.00) |
0.122 (1.00) |
0.0558 (1.00) |
1 (1.00) |
0.328 (1.00) |
14Q GAIN MUTATION ANALYSIS | 18 (3%) | 535 |
0.16 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.37 (1.00) |
0.0775 (1.00) |
0.447 (1.00) |
15Q GAIN MUTATION ANALYSIS | 24 (4%) | 529 |
0.402 (1.00) |
0.778 (1.00) |
0.833 (1.00) |
0.336 (1.00) |
0.346 (1.00) |
0.0443 (1.00) |
16P GAIN MUTATION ANALYSIS | 37 (7%) | 516 |
0.0321 (1.00) |
0.375 (1.00) |
0.163 (1.00) |
0.699 (1.00) |
1 (1.00) |
0.0446 (1.00) |
16Q GAIN MUTATION ANALYSIS | 36 (7%) | 517 |
0.122 (1.00) |
0.339 (1.00) |
0.378 (1.00) |
0.984 (1.00) |
1 (1.00) |
0.0624 (1.00) |
17P GAIN MUTATION ANALYSIS | 41 (7%) | 512 |
0.267 (1.00) |
0.336 (1.00) |
0.323 (1.00) |
0.982 (1.00) |
0.834 (1.00) |
0.482 (1.00) |
17Q GAIN MUTATION ANALYSIS | 53 (10%) | 500 |
0.0588 (1.00) |
0.11 (1.00) |
0.658 (1.00) |
0.678 (1.00) |
0.878 (1.00) |
0.436 (1.00) |
18P GAIN MUTATION ANALYSIS | 50 (9%) | 503 |
0.761 (1.00) |
0.669 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.462 (1.00) |
0.749 (1.00) |
18Q GAIN MUTATION ANALYSIS | 50 (9%) | 503 |
0.918 (1.00) |
0.387 (1.00) |
0.363 (1.00) |
0.248 (1.00) |
0.462 (1.00) |
0.522 (1.00) |
19P GAIN MUTATION ANALYSIS | 208 (38%) | 345 |
0.253 (1.00) |
0.949 (1.00) |
0.858 (1.00) |
0.641 (1.00) |
0.25 (1.00) |
0.569 (1.00) |
19Q GAIN MUTATION ANALYSIS | 182 (33%) | 371 |
0.364 (1.00) |
0.304 (1.00) |
1 (1.00) |
0.721 (1.00) |
0.853 (1.00) |
1 (1.00) |
21Q GAIN MUTATION ANALYSIS | 58 (10%) | 495 |
0.518 (1.00) |
0.0751 (1.00) |
0.777 (1.00) |
0.246 (1.00) |
0.455 (1.00) |
0.881 (1.00) |
22Q GAIN MUTATION ANALYSIS | 33 (6%) | 520 |
0.237 (1.00) |
0.73 (1.00) |
1 (1.00) |
0.446 (1.00) |
0.794 (1.00) |
0.846 (1.00) |
XQ GAIN MUTATION ANALYSIS | 17 (3%) | 536 |
0.841 (1.00) |
0.438 (1.00) |
0.805 (1.00) |
0.327 (1.00) |
0.211 (1.00) |
0.181 (1.00) |
1P LOSS MUTATION ANALYSIS | 14 (3%) | 539 |
0.211 (1.00) |
0.0574 (1.00) |
0.581 (1.00) |
0.84 (1.00) |
0.521 (1.00) |
0.381 (1.00) |
1Q LOSS MUTATION ANALYSIS | 13 (2%) | 540 |
0.653 (1.00) |
0.00809 (1.00) |
1 (1.00) |
0.178 (1.00) |
1 (1.00) |
0.236 (1.00) |
2P LOSS MUTATION ANALYSIS | 31 (6%) | 522 |
0.934 (1.00) |
0.202 (1.00) |
0.0367 (1.00) |
0.864 (1.00) |
1 (1.00) |
0.229 (1.00) |
2Q LOSS MUTATION ANALYSIS | 32 (6%) | 521 |
0.979 (1.00) |
0.333 (1.00) |
0.061 (1.00) |
0.625 (1.00) |
0.609 (1.00) |
0.0502 (1.00) |
3P LOSS MUTATION ANALYSIS | 38 (7%) | 515 |
0.26 (1.00) |
0.0373 (1.00) |
0.734 (1.00) |
0.767 (1.00) |
0.552 (1.00) |
0.0442 (1.00) |
3Q LOSS MUTATION ANALYSIS | 32 (6%) | 521 |
0.704 (1.00) |
0.42 (1.00) |
0.456 (1.00) |
0.908 (1.00) |
1 (1.00) |
0.326 (1.00) |
4P LOSS MUTATION ANALYSIS | 54 (10%) | 499 |
0.585 (1.00) |
0.483 (1.00) |
0.242 (1.00) |
0.354 (1.00) |
0.26 (1.00) |
0.645 (1.00) |
4Q LOSS MUTATION ANALYSIS | 54 (10%) | 499 |
0.132 (1.00) |
0.082 (1.00) |
1 (1.00) |
0.115 (1.00) |
0.767 (1.00) |
0.645 (1.00) |
5P LOSS MUTATION ANALYSIS | 44 (8%) | 509 |
0.0672 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.84 (1.00) |
1 (1.00) |
0.062 (1.00) |
5Q LOSS MUTATION ANALYSIS | 44 (8%) | 509 |
0.107 (1.00) |
0.325 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.499 (1.00) |
0.129 (1.00) |
6P LOSS MUTATION ANALYSIS | 83 (15%) | 470 |
0.0103 (1.00) |
0.475 (1.00) |
0.465 (1.00) |
0.952 (1.00) |
0.521 (1.00) |
0.606 (1.00) |
6Q LOSS MUTATION ANALYSIS | 120 (22%) | 433 |
0.335 (1.00) |
0.75 (1.00) |
0.246 (1.00) |
0.721 (1.00) |
0.297 (1.00) |
0.824 (1.00) |
7P LOSS MUTATION ANALYSIS | 8 (1%) | 545 |
0.372 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.628 (1.00) |
1 (1.00) |
0.445 (1.00) |
7Q LOSS MUTATION ANALYSIS | 6 (1%) | 547 |
0.544 (1.00) |
0.0995 (1.00) |
1 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.672 (1.00) |
8P LOSS MUTATION ANALYSIS | 59 (11%) | 494 |
0.44 (1.00) |
0.0874 (1.00) |
0.325 (1.00) |
0.934 (1.00) |
0.886 (1.00) |
0.554 (1.00) |
8Q LOSS MUTATION ANALYSIS | 45 (8%) | 508 |
0.185 (1.00) |
0.0529 (1.00) |
0.751 (1.00) |
0.608 (1.00) |
0.853 (1.00) |
0.867 (1.00) |
9P LOSS MUTATION ANALYSIS | 191 (35%) | 362 |
0.355 (1.00) |
0.543 (1.00) |
0.648 (1.00) |
0.975 (1.00) |
0.856 (1.00) |
0.441 (1.00) |
9Q LOSS MUTATION ANALYSIS | 85 (15%) | 468 |
0.308 (1.00) |
0.589 (1.00) |
0.28 (1.00) |
0.502 (1.00) |
0.914 (1.00) |
0.611 (1.00) |
11P LOSS MUTATION ANALYSIS | 96 (17%) | 457 |
0.151 (1.00) |
0.908 (1.00) |
0.0665 (1.00) |
0.878 (1.00) |
0.48 (1.00) |
0.466 (1.00) |
11Q LOSS MUTATION ANALYSIS | 91 (16%) | 462 |
0.828 (1.00) |
0.252 (1.00) |
0.349 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.172 (1.00) |
12P LOSS MUTATION ANALYSIS | 60 (11%) | 493 |
0.83 (1.00) |
0.522 (1.00) |
0.487 (1.00) |
0.535 (1.00) |
1 (1.00) |
1 (1.00) |
12Q LOSS MUTATION ANALYSIS | 57 (10%) | 496 |
0.919 (1.00) |
0.736 (1.00) |
0.775 (1.00) |
0.516 (1.00) |
0.579 (1.00) |
0.545 (1.00) |
13Q LOSS MUTATION ANALYSIS | 177 (32%) | 376 |
0.931 (1.00) |
0.859 (1.00) |
1 (1.00) |
0.717 (1.00) |
0.685 (1.00) |
0.43 (1.00) |
14Q LOSS MUTATION ANALYSIS | 144 (26%) | 409 |
0.92 (1.00) |
0.809 (1.00) |
0.692 (1.00) |
0.567 (1.00) |
0.121 (1.00) |
0.675 (1.00) |
15Q LOSS MUTATION ANALYSIS | 97 (18%) | 456 |
0.71 (1.00) |
0.0552 (1.00) |
0.424 (1.00) |
0.94 (1.00) |
0.309 (1.00) |
0.0921 (1.00) |
16P LOSS MUTATION ANALYSIS | 61 (11%) | 492 |
0.0811 (1.00) |
0.242 (1.00) |
0.89 (1.00) |
0.994 (1.00) |
0.264 (1.00) |
0.0787 (1.00) |
16Q LOSS MUTATION ANALYSIS | 79 (14%) | 474 |
0.0372 (1.00) |
0.955 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.364 (1.00) |
0.0496 (1.00) |
17P LOSS MUTATION ANALYSIS | 63 (11%) | 490 |
0.754 (1.00) |
0.402 (1.00) |
0.413 (1.00) |
0.493 (1.00) |
0.887 (1.00) |
0.195 (1.00) |
17Q LOSS MUTATION ANALYSIS | 41 (7%) | 512 |
0.931 (1.00) |
0.447 (1.00) |
0.619 (1.00) |
0.353 (1.00) |
0.834 (1.00) |
0.0343 (1.00) |
18P LOSS MUTATION ANALYSIS | 68 (12%) | 485 |
0.135 (1.00) |
0.836 (1.00) |
0.692 (1.00) |
0.493 (1.00) |
0.801 (1.00) |
0.889 (1.00) |
18Q LOSS MUTATION ANALYSIS | 60 (11%) | 493 |
0.305 (1.00) |
0.89 (1.00) |
0.89 (1.00) |
0.191 (1.00) |
0.886 (1.00) |
0.304 (1.00) |
19P LOSS MUTATION ANALYSIS | 28 (5%) | 525 |
0.412 (1.00) |
0.584 (1.00) |
0.435 (1.00) |
0.87 (1.00) |
0.548 (1.00) |
0.837 (1.00) |
19Q LOSS MUTATION ANALYSIS | 36 (7%) | 517 |
0.34 (1.00) |
0.451 (1.00) |
0.597 (1.00) |
0.734 (1.00) |
0.306 (1.00) |
0.714 (1.00) |
20P LOSS MUTATION ANALYSIS | 18 (3%) | 535 |
0.901 (1.00) |
0.273 (1.00) |
0.219 (1.00) |
0.714 (1.00) |
1 (1.00) |
0.8 (1.00) |
20Q LOSS MUTATION ANALYSIS | 17 (3%) | 536 |
0.95 (1.00) |
0.771 (1.00) |
0.129 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.79 (1.00) |
21Q LOSS MUTATION ANALYSIS | 40 (7%) | 513 |
0.761 (1.00) |
0.933 (1.00) |
0.503 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.215 (1.00) |
22Q LOSS MUTATION ANALYSIS | 175 (32%) | 378 |
0.383 (1.00) |
0.132 (1.00) |
0.925 (1.00) |
0.559 (1.00) |
0.81 (1.00) |
1 (1.00) |
XQ LOSS MUTATION ANALYSIS | 113 (20%) | 440 |
0.081 (1.00) |
0.475 (1.00) |
0.748 (1.00) |
0.482 (1.00) |
0.354 (1.00) |
0.425 (1.00) |
P value = 9.19e-05 (logrank test), Q value = 0.043
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 553 | 445 | 0.1 - 127.6 (9.9) |
7P GAIN MUTATED | 447 | 366 | 0.1 - 127.6 (9.6) |
7P GAIN WILD-TYPE | 106 | 79 | 0.2 - 108.8 (13.0) |
P value = 3.03e-06 (t-test), Q value = 0.0014
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
7P GAIN MUTATED | 447 | 59.7 (12.4) |
7P GAIN WILD-TYPE | 106 | 50.1 (19.3) |
P value = 0.000228 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 553 | 445 | 0.1 - 127.6 (9.9) |
7Q GAIN MUTATED | 451 | 367 | 0.1 - 127.6 (9.6) |
7Q GAIN WILD-TYPE | 102 | 78 | 0.2 - 108.8 (13.8) |
P value = 1.38e-05 (t-test), Q value = 0.0066
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
7Q GAIN MUTATED | 451 | 59.5 (12.2) |
7Q GAIN WILD-TYPE | 102 | 50.2 (20.1) |
P value = 0.00032 (t-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 77.4 (14.7) |
10P GAIN MUTATED | 11 | 80.0 (0.0) |
10P GAIN WILD-TYPE | 397 | 77.3 (14.9) |
P value = 5.28e-05 (t-test), Q value = 0.025
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
20P GAIN MUTATED | 209 | 60.9 (13.0) |
20P GAIN WILD-TYPE | 344 | 56.0 (15.0) |
P value = 0.000249 (t-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
20Q GAIN MUTATED | 207 | 60.6 (13.3) |
20Q GAIN WILD-TYPE | 346 | 56.1 (14.9) |
P value = 9.78e-06 (logrank test), Q value = 0.0047
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 553 | 445 | 0.1 - 127.6 (9.9) |
10P LOSS MUTATED | 460 | 376 | 0.1 - 127.6 (9.8) |
10P LOSS WILD-TYPE | 93 | 69 | 0.2 - 108.8 (12.7) |
P value = 6.53e-08 (t-test), Q value = 3.1e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
10P LOSS MUTATED | 460 | 59.8 (12.5) |
10P LOSS WILD-TYPE | 93 | 47.9 (18.9) |
P value = 6.88e-05 (logrank test), Q value = 0.033
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 553 | 445 | 0.1 - 127.6 (9.9) |
10Q LOSS MUTATED | 472 | 385 | 0.1 - 127.6 (9.8) |
10Q LOSS WILD-TYPE | 81 | 60 | 0.2 - 108.8 (12.0) |
P value = 1.16e-06 (t-test), Q value = 0.00055
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 553 | 57.8 (14.4) |
10Q LOSS MUTATED | 472 | 59.5 (12.9) |
10Q LOSS WILD-TYPE | 81 | 48.3 (18.6) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = GBM-TP.clin.merged.picked.txt
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Number of patients = 553
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Number of significantly arm-level cnvs = 80
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Number of selected clinical features = 6
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Exclude regions that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.