filterGenes: Filter out significant genes from meta-analysis results
In MetaIntegrator: Meta-Analysis of Gene Expression Data
Description
Usage
Arguments
Value
Note
Author(s)
See Also
Examples
Description
After the Meta-Analysis results have been written to the metaObject,
the results can be examined using different gene filtering criteria.
This function will use the given filterParameter to select genes that fulfill the filter conditions.
The function returns a modified version of the metaObject with results stored in metaObject$filterResults
Usage
1
2
3
filterGenes(metaObject, isLeaveOneOut = TRUE, effectSizeThresh = 0,
FDRThresh = 0.05, numberStudiesThresh = 1,
heterogeneityPvalThresh = 0)
Arguments
metaObject
a Meta object which must have the $originalData, $metaAnalysis populated
isLeaveOneOut
Do leave-one-out analysis on discovery datasets (default: TRUE). Needs at least 2 datasets for discovery.
effectSizeThresh
a gene is selected, if the absolute value of its effect size is above this threshold (default: 0)
FDRThresh
FDR cutoff: a gene is selected, if it has a p-value less than or equal to the FDR cutoff (default: 0.05)
numberStudiesThresh
number of studies in which a selected gene has to be significantly up/down regulated (default: 1)
heterogeneityPvalThresh
heterogeneity p-value cutoff (filter is off by default: heterogeneityPvalThresh = 0).
Genes with significant heterogeneity and, thus a significant (low) heterogeneity p-value, can be filtered out by using e.g.:
heterogeneityPvalThresh = 0.05 (removes all genes with heterogeneity p-value < 0.05)
Value
A modified version of the input metaObject with an additional filterObject stored within metaObject$filterResults
Note
Use checkDataObject(metaObject, "Meta", "Pre-Filter") to make sure your metaObject has the right format for filtering after running the meta-analysis with runMetaAnalysis().
Author(s)
Francesco Vallania
See Also
Examples
1
2
3
4
5
6
7
8
# filter genes with default settings
#(false discovery rate cutoff of 5 percent and WITH leave-one-out analysis)
testMetaObject <- filterGenes(tinyMetaObject)
summarizeFilterResults(testMetaObject, getMostRecentFilter(testMetaObject))
# filter genes with false discovery rate of 1 percent and WITHOUT leave-one-out analysis
testMetaObject <- filterGenes(testMetaObject, FDRThresh = 0.01, isLeaveOneOut = FALSE)
summarizeFilterResults(testMetaObject, getMostRecentFilter(testMetaObject))
Example output
$pos
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene27 1.1632133 0.10668133 1.107537e-27 1.849586e-25
Gene13 1.6290491 0.15140558 5.345649e-27 4.463617e-25
Gene136 0.8580906 0.09707125 9.588873e-19 5.337806e-17
Gene36 1.1852566 0.16003105 1.297580e-13 3.095656e-12
Gene26 1.0090138 0.13960649 4.917610e-13 1.026551e-11
Gene7 0.5477108 0.07994968 7.349266e-12 1.227327e-10
Gene17 1.1866787 0.17394874 8.978005e-12 1.363024e-10
Gene2 0.4889767 0.07490382 6.662646e-11 7.947585e-10
Gene24 1.0565405 0.17982915 4.222159e-09 4.406879e-08
Gene12 0.7934474 0.13754038 7.982286e-09 7.405788e-08
Gene35 1.0524923 0.20306169 2.182093e-07 1.401575e-06
Gene23 0.8803728 0.17123064 2.726343e-07 1.686294e-06
Gene166 0.7564151 0.15275607 7.353602e-07 4.234660e-06
Gene19 1.1567333 0.28325313 4.431586e-05 2.062866e-04
Gene42 0.7642982 0.21035216 2.796869e-04 1.167693e-03
Gene158 0.2827290 0.08251859 6.119842e-04 2.003948e-03
Gene8 0.7161901 0.26111085 6.090692e-03 1.564839e-02
Gene5 0.9963489 0.40438425 1.374472e-02 3.101849e-02
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene27 0.00000000 3 0.01310449 0.99346917 130.50116
Gene13 0.00000000 3 1.39880786 0.49688139 136.99524
Gene136 0.00000000 2 0.55258141 0.45726485 50.69783
Gene36 0.00000000 2 0.10687482 0.74373055 66.32116
Gene26 0.00000000 3 1.43300798 0.48845692 68.53009
Gene7 0.00000000 3 0.51993135 0.77107805 30.40995
Gene17 0.04541667 3 3.95629827 0.13832502 83.64513
Gene2 0.00000000 3 1.79835362 0.40690448 46.33389
Gene24 0.01187769 2 1.16373481 0.28069232 55.75905
Gene12 0.00000000 3 1.68690818 0.43022193 47.69750
Gene35 0.05411226 3 3.47629214 0.17584610 67.49148
Gene23 0.02431408 3 2.68341307 0.26139920 53.94667
Gene166 0.00000000 2 0.01079359 0.91725490 33.62254
Gene19 0.16536522 3 6.51555859 0.03847374 75.31925
Gene42 0.07733480 3 4.65980287 0.09730534 51.06609
Gene158 0.00000000 3 0.93875464 0.62539157 22.12530
Gene8 0.07887896 2 2.17204207 0.14053950 28.63867
Gene5 0.26893169 2 5.08417460 0.02414517 45.07051
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene27 1.008046e-25 8.417186e-24 1.818131e-02 0.9999999 1
Gene13 4.313804e-27 7.204053e-25 4.881354e-05 1.0000000 1
Gene136 2.581479e-10 2.268984e-09 7.865023e-04 0.9999999 1
Gene36 1.355405e-13 1.886272e-12 9.336704e-05 1.0000000 1
Gene26 8.182527e-13 9.760586e-12 6.352420e-03 1.0000000 1
Gene7 3.284592e-05 1.275644e-04 2.485254e-01 0.9997086 1
Gene17 6.298572e-16 2.103723e-14 1.365882e-04 1.0000000 1
Gene2 2.540272e-08 1.515091e-07 5.156880e-01 0.9976423 1
Gene24 2.252504e-11 2.285523e-10 3.895598e-05 1.0000000 1
Gene12 1.358008e-08 8.399530e-08 1.638100e-01 0.9999139 1
Gene35 1.335193e-12 1.486515e-11 1.005136e-04 1.0000000 1
Gene23 7.562101e-10 6.314354e-09 8.490221e-04 1.0000000 1
Gene166 8.905409e-07 4.131120e-06 1.187855e-02 0.9999824 1
Gene19 3.299192e-14 6.121834e-13 7.196461e-04 1.0000000 1
Gene42 2.872760e-09 2.180686e-08 2.106833e-01 0.9998199 1
Gene158 1.149163e-03 3.553893e-03 2.284344e+00 0.8917793 1
Gene8 9.256196e-06 3.770206e-05 3.485909e-03 0.9999985 1
Gene5 3.843979e-09 2.791063e-08 4.783197e-04 1.0000000 1
$neg
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene65 -0.9108702 0.11697029 6.851455e-15 2.860483e-13
Gene66 -0.5641520 0.07321384 1.302928e-14 4.351779e-13
Gene62 -0.7748318 0.10188377 2.847801e-14 7.926378e-13
Gene59 -0.5772361 0.08198619 1.913453e-12 3.550518e-11
Gene56 -0.4108498 0.06196003 3.336834e-11 4.643760e-10
Gene63 -0.3524544 0.05374244 5.445590e-11 6.995489e-10
Gene50 -0.5383657 0.08423914 1.648892e-10 1.835766e-09
Gene47 -1.0183475 0.18329790 2.765069e-08 2.308833e-07
Gene45 -0.7541341 0.13695479 3.661516e-08 2.911777e-07
Gene49 -0.4418702 0.08307571 1.044044e-07 7.264804e-07
Gene54 -0.4100211 0.08539501 1.575098e-06 8.768044e-06
Gene48 -0.8574953 0.20652024 3.294202e-05 1.618035e-04
Gene53 -0.3364151 0.09560700 4.336198e-04 1.684058e-03
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene65 0.000000000 2 0.06991577 0.7914595 0.001882666
Gene66 0.000000000 3 1.29765174 0.5226591 1.724806939
Gene62 0.000000000 3 0.73083855 0.6939057 0.084553697
Gene59 0.001354013 3 2.11946254 0.3465489 0.406169936
Gene56 0.000000000 3 0.16113556 0.9225924 12.254775610
Gene63 0.000000000 3 0.06741452 0.9668545 5.384946249
Gene50 0.000000000 3 0.01140394 0.9943143 3.306203329
Gene47 0.034872885 3 2.98058253 0.2253070 0.009530614
Gene45 0.000000000 3 1.85391891 0.3957552 0.209446828
Gene49 0.000000000 3 0.66566962 0.7168886 1.319780091
Gene54 0.004890694 3 2.40751805 0.3000641 6.224063539
Gene48 0.060165779 3 3.70556346 0.1568004 0.001851266
Gene53 0.006424830 3 2.43830766 0.2954801 2.600141587
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene65 0.99999956 1.0000000 57.67330 8.936165e-12 3.730849e-10
Gene66 0.94319010 1.0000000 45.26015 4.154898e-08 7.709644e-07
Gene62 0.99998780 1.0000000 50.38042 3.943775e-09 1.097684e-07
Gene59 0.99880030 1.0000000 42.66136 1.360968e-07 1.623441e-06
Gene56 0.05652052 0.1329426 80.04266 3.501101e-15 5.846838e-13
Gene63 0.49547010 0.7512644 42.77509 1.292275e-07 1.623441e-06
Gene50 0.76954907 0.9662759 48.97484 7.542890e-09 1.574578e-07
Gene47 0.99999998 1.0000000 68.42147 8.612657e-13 5.479374e-11
Gene45 0.99982301 1.0000000 44.70639 5.352895e-08 8.126668e-07
Gene49 0.97055581 1.0000000 29.09835 5.828432e-05 3.604993e-04
Gene54 0.39856430 0.6656024 68.13827 9.843187e-13 5.479374e-11
Gene48 1.00000000 1.0000000 49.35643 6.326239e-09 1.509260e-07
Gene53 0.85709619 0.9949102 33.37729 8.870716e-06 7.407048e-05
$pos
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene27 1.1632133 0.10668133 1.107537e-27 1.849586e-25
Gene13 1.6290491 0.15140558 5.345649e-27 4.463617e-25
Gene136 0.8580906 0.09707125 9.588873e-19 5.337806e-17
Gene36 1.1852566 0.16003105 1.297580e-13 3.095656e-12
Gene26 1.0090138 0.13960649 4.917610e-13 1.026551e-11
Gene7 0.5477108 0.07994968 7.349266e-12 1.227327e-10
Gene17 1.1866787 0.17394874 8.978005e-12 1.363024e-10
Gene2 0.4889767 0.07490382 6.662646e-11 7.947585e-10
Gene24 1.0565405 0.17982915 4.222159e-09 4.406879e-08
Gene6 0.4004258 0.06841750 4.837099e-09 4.751739e-08
Gene12 0.7934474 0.13754038 7.982286e-09 7.405788e-08
Gene3 0.4438534 0.07987475 2.746596e-08 2.308833e-07
Gene38 0.4559432 0.08320960 4.266408e-08 3.238592e-07
Gene11 0.6211862 0.11425512 5.423535e-08 3.937958e-07
Gene35 1.0524923 0.20306169 2.182093e-07 1.401575e-06
Gene23 0.8803728 0.17123064 2.726343e-07 1.686294e-06
Gene93 0.3583787 0.07225905 7.062477e-07 4.212263e-06
Gene166 0.7564151 0.15275607 7.353602e-07 4.234660e-06
Gene4 0.4287458 0.10065580 2.048625e-05 1.069126e-04
Gene31 0.4467658 0.10659186 2.772767e-05 1.403188e-04
Gene19 1.1567333 0.28325313 4.431586e-05 2.062866e-04
Gene37 0.7870975 0.19277700 4.446897e-05 2.062866e-04
Gene10 0.6429299 0.17303913 2.027882e-04 8.776422e-04
Gene34 1.1208855 0.30189556 2.049584e-04 8.776422e-04
Gene42 0.7642982 0.21035216 2.796869e-04 1.167693e-03
Gene25 0.4881113 0.13467637 2.897138e-04 1.180054e-03
Gene30 0.7777747 0.21578750 3.129296e-04 1.244268e-03
Gene33 0.8178688 0.23333163 4.563032e-04 1.731878e-03
Gene135 0.4686475 0.13432041 4.847821e-04 1.752801e-03
Gene1 0.5197875 0.15006606 5.327516e-04 1.835247e-03
Gene114 0.3260202 0.09420254 5.384857e-04 1.835247e-03
Gene158 0.2827290 0.08251859 6.119842e-04 2.003948e-03
Gene40 0.5474666 0.17594130 1.860490e-03 5.649124e-03
Gene118 0.2877988 0.09441442 2.301784e-03 6.691218e-03
Gene39 0.8471309 0.27816957 2.323896e-03 6.691218e-03
Gene28 1.3037942 0.43361686 2.640234e-03 7.473204e-03
Gene22 0.4003222 0.13411925 2.837429e-03 7.897512e-03
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene27 0.000000000 3 0.01310449 9.934692e-01 130.50116
Gene13 0.000000000 3 1.39880786 4.968814e-01 136.99524
Gene136 0.000000000 2 0.55258141 4.572648e-01 50.69783
Gene36 0.000000000 2 0.10687482 7.437306e-01 66.32116
Gene26 0.000000000 3 1.43300798 4.884569e-01 68.53009
Gene7 0.000000000 3 0.51993135 7.710781e-01 30.40995
Gene17 0.045416668 3 3.95629827 1.383250e-01 83.64513
Gene2 0.000000000 3 1.79835362 4.069045e-01 46.33389
Gene24 0.011877692 2 1.16373481 2.806923e-01 55.75905
Gene6 0.000000000 3 0.36051385 8.350556e-01 37.80720
Gene12 0.000000000 3 1.68690818 4.302219e-01 47.69750
Gene3 0.000000000 3 0.76755671 6.812824e-01 41.28880
Gene38 0.000000000 2 0.53947274 4.626513e-01 55.69202
Gene11 0.000000000 2 0.54593019 4.599854e-01 38.79696
Gene35 0.054112261 3 3.47629214 1.758461e-01 67.49148
Gene23 0.024314077 3 2.68341307 2.613992e-01 53.94667
Gene93 0.000000000 3 0.18956953 9.095687e-01 21.27196
Gene166 0.000000000 2 0.01079359 9.172549e-01 33.62254
Gene4 0.000000000 3 0.27830251 8.700964e-01 45.22316
Gene31 0.000000000 3 1.95506469 3.762384e-01 39.55535
Gene19 0.165365217 3 6.51555859 3.847374e-02 75.31925
Gene37 0.045039411 3 3.28117565 1.938660e-01 49.24252
Gene10 NA 1 NA NA 18.51410
Gene34 0.198627623 3 7.51628459 2.332703e-02 77.07957
Gene42 0.077334800 3 4.65980287 9.730534e-02 51.06609
Gene25 0.000000000 3 1.97606958 3.723076e-01 26.55541
Gene30 0.085724975 3 5.29573687 7.080197e-02 49.85145
Gene33 0.092667138 3 4.60495136 1.000109e-01 45.43672
Gene135 0.000000000 3 1.01865151 6.009006e-01 23.72138
Gene1 0.000000000 2 0.25062746 6.166336e-01 20.17430
Gene114 0.001100199 2 1.03902949 3.080473e-01 33.43405
Gene158 0.000000000 3 0.93875464 6.253916e-01 22.12530
Gene40 0.040840808 3 3.36660316 1.857597e-01 41.63561
Gene118 0.000000000 2 0.75509479 3.848680e-01 38.01804
Gene39 0.096779731 2 2.50866796 1.132216e-01 47.42637
Gene28 0.505866869 3 23.16583674 9.324004e-06 93.14784
Gene22 0.000000000 3 1.91661515 3.835415e-01 20.03029
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene27 1.008046e-25 8.417186e-24 1.818131e-02 0.9999999 1.0000000
Gene13 4.313804e-27 7.204053e-25 4.881354e-05 1.0000000 1.0000000
Gene136 2.581479e-10 2.268984e-09 7.865023e-04 0.9999999 1.0000000
Gene36 1.355405e-13 1.886272e-12 9.336704e-05 1.0000000 1.0000000
Gene26 8.182527e-13 9.760586e-12 6.352420e-03 1.0000000 1.0000000
Gene7 3.284592e-05 1.275644e-04 2.485254e-01 0.9997086 1.0000000
Gene17 6.298572e-16 2.103723e-14 1.365882e-04 1.0000000 1.0000000
Gene2 2.540272e-08 1.515091e-07 5.156880e-01 0.9976423 1.0000000
Gene24 2.252504e-11 2.285523e-10 3.895598e-05 1.0000000 1.0000000
Gene6 1.225177e-06 5.384330e-06 2.599598e+00 0.8571588 1.0000000
Gene12 1.358008e-08 8.399530e-08 1.638100e-01 0.9999139 1.0000000
Gene3 2.540029e-07 1.247602e-06 1.245893e+00 0.9745573 1.0000000
Gene38 2.326581e-11 2.285523e-10 1.483708e+00 0.8295234 1.0000000
Gene11 7.672654e-08 4.133333e-07 2.089953e-01 0.9949060 1.0000000
Gene35 1.335193e-12 1.486515e-11 1.005136e-04 1.0000000 1.0000000
Gene23 7.562101e-10 6.314354e-09 8.490221e-04 1.0000000 1.0000000
Gene93 1.639168e-03 4.802476e-03 1.027727e+00 0.9845394 1.0000000
Gene166 8.905409e-07 4.131120e-06 1.187855e-02 0.9999824 1.0000000
Gene4 4.225846e-08 2.352388e-07 2.283942e+00 0.8918212 1.0000000
Gene31 5.569724e-07 2.657554e-06 1.677464e+00 0.9468478 1.0000000
Gene19 3.299192e-14 6.121834e-13 7.196461e-04 1.0000000 1.0000000
Gene37 6.667383e-09 4.282512e-08 2.388357e-01 0.9997404 1.0000000
Gene10 9.543653e-05 3.391043e-04 1.908822e-04 0.9999046 1.0000000
Gene34 1.431199e-14 2.987627e-13 1.971146e-02 0.9999998 1.0000000
Gene42 2.872760e-09 2.180686e-08 2.106833e-01 0.9998199 1.0000000
Gene25 1.753789e-04 6.101726e-04 8.916588e-02 0.9999857 1.0000000
Gene30 5.034678e-09 3.503297e-08 1.572375e-01 0.9999236 1.0000000
Gene33 3.832244e-08 2.206844e-07 1.217543e-02 1.0000000 1.0000000
Gene135 5.876027e-04 1.887109e-03 4.204237e-01 0.9986765 1.0000000
Gene1 4.613445e-04 1.540891e-03 3.866447e-02 0.9998155 1.0000000
Gene114 9.733721e-07 4.393328e-06 2.547132e+00 0.6362164 1.0000000
Gene158 1.149163e-03 3.553893e-03 2.284344e+00 0.8917793 1.0000000
Gene40 2.169930e-07 1.098116e-06 7.341502e-01 0.9937242 1.0000000
Gene118 1.111000e-07 5.798033e-07 3.971867e+00 0.4098266 0.7690004
Gene39 1.242866e-09 9.883743e-09 9.921372e-02 0.9988095 1.0000000
Gene28 6.715876e-18 2.803878e-16 2.377650e-04 1.0000000 1.0000000
Gene22 2.735221e-03 7.613031e-03 1.261746e+00 0.9737251 1.0000000
$neg
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene65 -0.9108702 0.11697029 6.851455e-15 2.860483e-13
Gene66 -0.5641520 0.07321384 1.302928e-14 4.351779e-13
Gene62 -0.7748318 0.10188377 2.847801e-14 7.926378e-13
Gene59 -0.5772361 0.08198619 1.913453e-12 3.550518e-11
Gene56 -0.4108498 0.06196003 3.336834e-11 4.643760e-10
Gene63 -0.3524544 0.05374244 5.445590e-11 6.995489e-10
Gene50 -0.5383657 0.08423914 1.648892e-10 1.835766e-09
Gene47 -1.0183475 0.18329790 2.765069e-08 2.308833e-07
Gene45 -0.7541341 0.13695479 3.661516e-08 2.911777e-07
Gene49 -0.4418702 0.08307571 1.044044e-07 7.264804e-07
Gene44 -0.5543407 0.10655823 1.969085e-07 1.315349e-06
Gene54 -0.4100211 0.08539501 1.575098e-06 8.768044e-06
Gene94 -0.2384120 0.05366514 8.888416e-06 4.788276e-05
Gene48 -0.8574953 0.20652024 3.294202e-05 1.618035e-04
Gene61 -0.2708759 0.06990700 1.067109e-04 4.816413e-04
Gene53 -0.3364151 0.09560700 4.336198e-04 1.684058e-03
Gene55 -0.6013534 0.17249691 4.899908e-04 1.752801e-03
Gene67 -0.3553792 0.10199248 4.933032e-04 1.752801e-03
Gene51 -0.5241454 0.15231843 5.793205e-04 1.934931e-03
Gene64 -0.5057346 0.14967960 7.280804e-04 2.338258e-03
Gene46 -0.6010021 0.17889758 7.809045e-04 2.460586e-03
Gene52 -0.4259713 0.13418501 1.500909e-03 4.641700e-03
Gene123 -0.2227457 0.07203590 1.987131e-03 5.925908e-03
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene65 0.000000000 2 0.06991577 0.79145946 1.882666e-03
Gene66 0.000000000 3 1.29765174 0.52265909 1.724807e+00
Gene62 0.000000000 3 0.73083855 0.69390565 8.455370e-02
Gene59 0.001354013 3 2.11946254 0.34654893 4.061699e-01
Gene56 0.000000000 3 0.16113556 0.92259237 1.225478e+01
Gene63 0.000000000 3 0.06741452 0.96685450 5.384946e+00
Gene50 0.000000000 3 0.01140394 0.99431425 3.306203e+00
Gene47 0.034872885 3 2.98058253 0.22530702 9.530614e-03
Gene45 0.000000000 3 1.85391891 0.39575519 2.094468e-01
Gene49 0.000000000 3 0.66566962 0.71688861 1.319780e+00
Gene44 0.000000000 3 0.01612983 0.99196752 2.257258e-01
Gene54 0.004890694 3 2.40751805 0.30006414 6.224064e+00
Gene94 0.000000000 3 0.23544594 0.88894228 1.582510e+01
Gene48 0.060165779 3 3.70556346 0.15680038 1.851266e-03
Gene61 0.000000000 3 0.08418243 0.95878232 4.167637e+00
Gene53 0.006424830 3 2.43830766 0.29548009 2.600142e+00
Gene55 NA 1 NA NA 4.650652e-04
Gene67 0.005248733 3 2.27453415 0.32069426 2.845783e+00
Gene51 0.038950780 3 4.61057118 0.09973031 4.096826e+00
Gene64 0.035537111 3 4.28700516 0.11724347 1.658011e+00
Gene46 0.043985144 3 3.49979348 0.17379189 2.995090e-01
Gene52 0.000000000 3 0.12417687 0.93979977 3.019494e-01
Gene123 0.000000000 3 0.13812441 0.93326863 4.624696e+00
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene65 0.99999956 1.00000000 57.67330 8.936165e-12 3.730849e-10
Gene66 0.94319010 1.00000000 45.26015 4.154898e-08 7.709644e-07
Gene62 0.99998780 1.00000000 50.38042 3.943775e-09 1.097684e-07
Gene59 0.99880030 1.00000000 42.66136 1.360968e-07 1.623441e-06
Gene56 0.05652052 0.13294264 80.04266 3.501101e-15 5.846838e-13
Gene63 0.49547010 0.75126436 42.77509 1.292275e-07 1.623441e-06
Gene50 0.76954907 0.96627590 48.97484 7.542890e-09 1.574578e-07
Gene47 0.99999998 1.00000000 68.42147 8.612657e-13 5.479374e-11
Gene45 0.99982301 1.00000000 44.70639 5.352895e-08 8.126668e-07
Gene49 0.97055581 1.00000000 29.09835 5.828432e-05 3.604993e-04
Gene44 0.99977979 1.00000000 40.33075 3.921747e-07 4.093323e-06
Gene54 0.39856430 0.66560238 68.13827 9.843187e-13 5.479374e-11
Gene94 0.01472418 0.03782983 28.37235 7.994089e-05 4.450043e-04
Gene48 1.00000000 1.00000000 49.35643 6.326239e-09 1.509260e-07
Gene61 0.65400217 0.86575799 28.42636 7.808666e-05 4.450043e-04
Gene53 0.85709619 0.99491018 33.37729 8.870716e-06 7.407048e-05
Gene55 0.99976749 1.00000000 16.73319 2.325055e-04 1.210977e-03
Gene67 0.82793888 0.99471793 26.80175 1.577287e-04 8.496998e-04
Gene51 0.66357498 0.86575799 51.90828 1.945708e-09 6.498665e-08
Gene64 0.94831664 1.00000000 44.90487 4.888401e-08 8.126668e-07
Gene46 0.99949951 1.00000000 42.75611 1.303499e-07 1.623441e-06
Gene52 0.99948764 1.00000000 20.49784 2.257149e-03 9.912288e-03
Gene123 0.59276699 0.80481371 32.54177 1.284392e-05 1.013635e-04
MetaIntegrator documentation built on March 26, 2020, 6:29 p.m.
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Description Usage Arguments Value Note Author(s) See Also Examples
Description
After the Meta-Analysis results have been written to the metaObject,
the results can be examined using different gene filtering criteria.
This function will use the given filterParameter to select genes that fulfill the filter conditions.
The function returns a modified version of the metaObject with results stored in metaObject$filterResults
Usage
1 2 3 | filterGenes(metaObject, isLeaveOneOut = TRUE, effectSizeThresh = 0,
FDRThresh = 0.05, numberStudiesThresh = 1,
heterogeneityPvalThresh = 0)
|
Arguments
metaObject |
a Meta object which must have the |
isLeaveOneOut |
Do leave-one-out analysis on discovery datasets (default: TRUE). Needs at least 2 datasets for discovery. |
effectSizeThresh |
a gene is selected, if the absolute value of its effect size is above this threshold (default: 0) |
FDRThresh |
FDR cutoff: a gene is selected, if it has a p-value less than or equal to the FDR cutoff (default: 0.05) |
numberStudiesThresh |
number of studies in which a selected gene has to be significantly up/down regulated (default: 1) |
heterogeneityPvalThresh |
heterogeneity p-value cutoff (filter is off by default: |
Value
A modified version of the input metaObject with an additional filterObject stored within metaObject$filterResults
Note
Use checkDataObject(metaObject, "Meta", "Pre-Filter") to make sure your metaObject has the right format for filtering after running the meta-analysis with runMetaAnalysis().
Author(s)
Francesco Vallania
See Also
Examples
1 2 3 4 5 6 7 8 | # filter genes with default settings
#(false discovery rate cutoff of 5 percent and WITH leave-one-out analysis)
testMetaObject <- filterGenes(tinyMetaObject)
summarizeFilterResults(testMetaObject, getMostRecentFilter(testMetaObject))
# filter genes with false discovery rate of 1 percent and WITHOUT leave-one-out analysis
testMetaObject <- filterGenes(testMetaObject, FDRThresh = 0.01, isLeaveOneOut = FALSE)
summarizeFilterResults(testMetaObject, getMostRecentFilter(testMetaObject))
|
Example output
$pos
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene27 1.1632133 0.10668133 1.107537e-27 1.849586e-25
Gene13 1.6290491 0.15140558 5.345649e-27 4.463617e-25
Gene136 0.8580906 0.09707125 9.588873e-19 5.337806e-17
Gene36 1.1852566 0.16003105 1.297580e-13 3.095656e-12
Gene26 1.0090138 0.13960649 4.917610e-13 1.026551e-11
Gene7 0.5477108 0.07994968 7.349266e-12 1.227327e-10
Gene17 1.1866787 0.17394874 8.978005e-12 1.363024e-10
Gene2 0.4889767 0.07490382 6.662646e-11 7.947585e-10
Gene24 1.0565405 0.17982915 4.222159e-09 4.406879e-08
Gene12 0.7934474 0.13754038 7.982286e-09 7.405788e-08
Gene35 1.0524923 0.20306169 2.182093e-07 1.401575e-06
Gene23 0.8803728 0.17123064 2.726343e-07 1.686294e-06
Gene166 0.7564151 0.15275607 7.353602e-07 4.234660e-06
Gene19 1.1567333 0.28325313 4.431586e-05 2.062866e-04
Gene42 0.7642982 0.21035216 2.796869e-04 1.167693e-03
Gene158 0.2827290 0.08251859 6.119842e-04 2.003948e-03
Gene8 0.7161901 0.26111085 6.090692e-03 1.564839e-02
Gene5 0.9963489 0.40438425 1.374472e-02 3.101849e-02
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene27 0.00000000 3 0.01310449 0.99346917 130.50116
Gene13 0.00000000 3 1.39880786 0.49688139 136.99524
Gene136 0.00000000 2 0.55258141 0.45726485 50.69783
Gene36 0.00000000 2 0.10687482 0.74373055 66.32116
Gene26 0.00000000 3 1.43300798 0.48845692 68.53009
Gene7 0.00000000 3 0.51993135 0.77107805 30.40995
Gene17 0.04541667 3 3.95629827 0.13832502 83.64513
Gene2 0.00000000 3 1.79835362 0.40690448 46.33389
Gene24 0.01187769 2 1.16373481 0.28069232 55.75905
Gene12 0.00000000 3 1.68690818 0.43022193 47.69750
Gene35 0.05411226 3 3.47629214 0.17584610 67.49148
Gene23 0.02431408 3 2.68341307 0.26139920 53.94667
Gene166 0.00000000 2 0.01079359 0.91725490 33.62254
Gene19 0.16536522 3 6.51555859 0.03847374 75.31925
Gene42 0.07733480 3 4.65980287 0.09730534 51.06609
Gene158 0.00000000 3 0.93875464 0.62539157 22.12530
Gene8 0.07887896 2 2.17204207 0.14053950 28.63867
Gene5 0.26893169 2 5.08417460 0.02414517 45.07051
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene27 1.008046e-25 8.417186e-24 1.818131e-02 0.9999999 1
Gene13 4.313804e-27 7.204053e-25 4.881354e-05 1.0000000 1
Gene136 2.581479e-10 2.268984e-09 7.865023e-04 0.9999999 1
Gene36 1.355405e-13 1.886272e-12 9.336704e-05 1.0000000 1
Gene26 8.182527e-13 9.760586e-12 6.352420e-03 1.0000000 1
Gene7 3.284592e-05 1.275644e-04 2.485254e-01 0.9997086 1
Gene17 6.298572e-16 2.103723e-14 1.365882e-04 1.0000000 1
Gene2 2.540272e-08 1.515091e-07 5.156880e-01 0.9976423 1
Gene24 2.252504e-11 2.285523e-10 3.895598e-05 1.0000000 1
Gene12 1.358008e-08 8.399530e-08 1.638100e-01 0.9999139 1
Gene35 1.335193e-12 1.486515e-11 1.005136e-04 1.0000000 1
Gene23 7.562101e-10 6.314354e-09 8.490221e-04 1.0000000 1
Gene166 8.905409e-07 4.131120e-06 1.187855e-02 0.9999824 1
Gene19 3.299192e-14 6.121834e-13 7.196461e-04 1.0000000 1
Gene42 2.872760e-09 2.180686e-08 2.106833e-01 0.9998199 1
Gene158 1.149163e-03 3.553893e-03 2.284344e+00 0.8917793 1
Gene8 9.256196e-06 3.770206e-05 3.485909e-03 0.9999985 1
Gene5 3.843979e-09 2.791063e-08 4.783197e-04 1.0000000 1
$neg
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene65 -0.9108702 0.11697029 6.851455e-15 2.860483e-13
Gene66 -0.5641520 0.07321384 1.302928e-14 4.351779e-13
Gene62 -0.7748318 0.10188377 2.847801e-14 7.926378e-13
Gene59 -0.5772361 0.08198619 1.913453e-12 3.550518e-11
Gene56 -0.4108498 0.06196003 3.336834e-11 4.643760e-10
Gene63 -0.3524544 0.05374244 5.445590e-11 6.995489e-10
Gene50 -0.5383657 0.08423914 1.648892e-10 1.835766e-09
Gene47 -1.0183475 0.18329790 2.765069e-08 2.308833e-07
Gene45 -0.7541341 0.13695479 3.661516e-08 2.911777e-07
Gene49 -0.4418702 0.08307571 1.044044e-07 7.264804e-07
Gene54 -0.4100211 0.08539501 1.575098e-06 8.768044e-06
Gene48 -0.8574953 0.20652024 3.294202e-05 1.618035e-04
Gene53 -0.3364151 0.09560700 4.336198e-04 1.684058e-03
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene65 0.000000000 2 0.06991577 0.7914595 0.001882666
Gene66 0.000000000 3 1.29765174 0.5226591 1.724806939
Gene62 0.000000000 3 0.73083855 0.6939057 0.084553697
Gene59 0.001354013 3 2.11946254 0.3465489 0.406169936
Gene56 0.000000000 3 0.16113556 0.9225924 12.254775610
Gene63 0.000000000 3 0.06741452 0.9668545 5.384946249
Gene50 0.000000000 3 0.01140394 0.9943143 3.306203329
Gene47 0.034872885 3 2.98058253 0.2253070 0.009530614
Gene45 0.000000000 3 1.85391891 0.3957552 0.209446828
Gene49 0.000000000 3 0.66566962 0.7168886 1.319780091
Gene54 0.004890694 3 2.40751805 0.3000641 6.224063539
Gene48 0.060165779 3 3.70556346 0.1568004 0.001851266
Gene53 0.006424830 3 2.43830766 0.2954801 2.600141587
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene65 0.99999956 1.0000000 57.67330 8.936165e-12 3.730849e-10
Gene66 0.94319010 1.0000000 45.26015 4.154898e-08 7.709644e-07
Gene62 0.99998780 1.0000000 50.38042 3.943775e-09 1.097684e-07
Gene59 0.99880030 1.0000000 42.66136 1.360968e-07 1.623441e-06
Gene56 0.05652052 0.1329426 80.04266 3.501101e-15 5.846838e-13
Gene63 0.49547010 0.7512644 42.77509 1.292275e-07 1.623441e-06
Gene50 0.76954907 0.9662759 48.97484 7.542890e-09 1.574578e-07
Gene47 0.99999998 1.0000000 68.42147 8.612657e-13 5.479374e-11
Gene45 0.99982301 1.0000000 44.70639 5.352895e-08 8.126668e-07
Gene49 0.97055581 1.0000000 29.09835 5.828432e-05 3.604993e-04
Gene54 0.39856430 0.6656024 68.13827 9.843187e-13 5.479374e-11
Gene48 1.00000000 1.0000000 49.35643 6.326239e-09 1.509260e-07
Gene53 0.85709619 0.9949102 33.37729 8.870716e-06 7.407048e-05
$pos
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene27 1.1632133 0.10668133 1.107537e-27 1.849586e-25
Gene13 1.6290491 0.15140558 5.345649e-27 4.463617e-25
Gene136 0.8580906 0.09707125 9.588873e-19 5.337806e-17
Gene36 1.1852566 0.16003105 1.297580e-13 3.095656e-12
Gene26 1.0090138 0.13960649 4.917610e-13 1.026551e-11
Gene7 0.5477108 0.07994968 7.349266e-12 1.227327e-10
Gene17 1.1866787 0.17394874 8.978005e-12 1.363024e-10
Gene2 0.4889767 0.07490382 6.662646e-11 7.947585e-10
Gene24 1.0565405 0.17982915 4.222159e-09 4.406879e-08
Gene6 0.4004258 0.06841750 4.837099e-09 4.751739e-08
Gene12 0.7934474 0.13754038 7.982286e-09 7.405788e-08
Gene3 0.4438534 0.07987475 2.746596e-08 2.308833e-07
Gene38 0.4559432 0.08320960 4.266408e-08 3.238592e-07
Gene11 0.6211862 0.11425512 5.423535e-08 3.937958e-07
Gene35 1.0524923 0.20306169 2.182093e-07 1.401575e-06
Gene23 0.8803728 0.17123064 2.726343e-07 1.686294e-06
Gene93 0.3583787 0.07225905 7.062477e-07 4.212263e-06
Gene166 0.7564151 0.15275607 7.353602e-07 4.234660e-06
Gene4 0.4287458 0.10065580 2.048625e-05 1.069126e-04
Gene31 0.4467658 0.10659186 2.772767e-05 1.403188e-04
Gene19 1.1567333 0.28325313 4.431586e-05 2.062866e-04
Gene37 0.7870975 0.19277700 4.446897e-05 2.062866e-04
Gene10 0.6429299 0.17303913 2.027882e-04 8.776422e-04
Gene34 1.1208855 0.30189556 2.049584e-04 8.776422e-04
Gene42 0.7642982 0.21035216 2.796869e-04 1.167693e-03
Gene25 0.4881113 0.13467637 2.897138e-04 1.180054e-03
Gene30 0.7777747 0.21578750 3.129296e-04 1.244268e-03
Gene33 0.8178688 0.23333163 4.563032e-04 1.731878e-03
Gene135 0.4686475 0.13432041 4.847821e-04 1.752801e-03
Gene1 0.5197875 0.15006606 5.327516e-04 1.835247e-03
Gene114 0.3260202 0.09420254 5.384857e-04 1.835247e-03
Gene158 0.2827290 0.08251859 6.119842e-04 2.003948e-03
Gene40 0.5474666 0.17594130 1.860490e-03 5.649124e-03
Gene118 0.2877988 0.09441442 2.301784e-03 6.691218e-03
Gene39 0.8471309 0.27816957 2.323896e-03 6.691218e-03
Gene28 1.3037942 0.43361686 2.640234e-03 7.473204e-03
Gene22 0.4003222 0.13411925 2.837429e-03 7.897512e-03
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene27 0.000000000 3 0.01310449 9.934692e-01 130.50116
Gene13 0.000000000 3 1.39880786 4.968814e-01 136.99524
Gene136 0.000000000 2 0.55258141 4.572648e-01 50.69783
Gene36 0.000000000 2 0.10687482 7.437306e-01 66.32116
Gene26 0.000000000 3 1.43300798 4.884569e-01 68.53009
Gene7 0.000000000 3 0.51993135 7.710781e-01 30.40995
Gene17 0.045416668 3 3.95629827 1.383250e-01 83.64513
Gene2 0.000000000 3 1.79835362 4.069045e-01 46.33389
Gene24 0.011877692 2 1.16373481 2.806923e-01 55.75905
Gene6 0.000000000 3 0.36051385 8.350556e-01 37.80720
Gene12 0.000000000 3 1.68690818 4.302219e-01 47.69750
Gene3 0.000000000 3 0.76755671 6.812824e-01 41.28880
Gene38 0.000000000 2 0.53947274 4.626513e-01 55.69202
Gene11 0.000000000 2 0.54593019 4.599854e-01 38.79696
Gene35 0.054112261 3 3.47629214 1.758461e-01 67.49148
Gene23 0.024314077 3 2.68341307 2.613992e-01 53.94667
Gene93 0.000000000 3 0.18956953 9.095687e-01 21.27196
Gene166 0.000000000 2 0.01079359 9.172549e-01 33.62254
Gene4 0.000000000 3 0.27830251 8.700964e-01 45.22316
Gene31 0.000000000 3 1.95506469 3.762384e-01 39.55535
Gene19 0.165365217 3 6.51555859 3.847374e-02 75.31925
Gene37 0.045039411 3 3.28117565 1.938660e-01 49.24252
Gene10 NA 1 NA NA 18.51410
Gene34 0.198627623 3 7.51628459 2.332703e-02 77.07957
Gene42 0.077334800 3 4.65980287 9.730534e-02 51.06609
Gene25 0.000000000 3 1.97606958 3.723076e-01 26.55541
Gene30 0.085724975 3 5.29573687 7.080197e-02 49.85145
Gene33 0.092667138 3 4.60495136 1.000109e-01 45.43672
Gene135 0.000000000 3 1.01865151 6.009006e-01 23.72138
Gene1 0.000000000 2 0.25062746 6.166336e-01 20.17430
Gene114 0.001100199 2 1.03902949 3.080473e-01 33.43405
Gene158 0.000000000 3 0.93875464 6.253916e-01 22.12530
Gene40 0.040840808 3 3.36660316 1.857597e-01 41.63561
Gene118 0.000000000 2 0.75509479 3.848680e-01 38.01804
Gene39 0.096779731 2 2.50866796 1.132216e-01 47.42637
Gene28 0.505866869 3 23.16583674 9.324004e-06 93.14784
Gene22 0.000000000 3 1.91661515 3.835415e-01 20.03029
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene27 1.008046e-25 8.417186e-24 1.818131e-02 0.9999999 1.0000000
Gene13 4.313804e-27 7.204053e-25 4.881354e-05 1.0000000 1.0000000
Gene136 2.581479e-10 2.268984e-09 7.865023e-04 0.9999999 1.0000000
Gene36 1.355405e-13 1.886272e-12 9.336704e-05 1.0000000 1.0000000
Gene26 8.182527e-13 9.760586e-12 6.352420e-03 1.0000000 1.0000000
Gene7 3.284592e-05 1.275644e-04 2.485254e-01 0.9997086 1.0000000
Gene17 6.298572e-16 2.103723e-14 1.365882e-04 1.0000000 1.0000000
Gene2 2.540272e-08 1.515091e-07 5.156880e-01 0.9976423 1.0000000
Gene24 2.252504e-11 2.285523e-10 3.895598e-05 1.0000000 1.0000000
Gene6 1.225177e-06 5.384330e-06 2.599598e+00 0.8571588 1.0000000
Gene12 1.358008e-08 8.399530e-08 1.638100e-01 0.9999139 1.0000000
Gene3 2.540029e-07 1.247602e-06 1.245893e+00 0.9745573 1.0000000
Gene38 2.326581e-11 2.285523e-10 1.483708e+00 0.8295234 1.0000000
Gene11 7.672654e-08 4.133333e-07 2.089953e-01 0.9949060 1.0000000
Gene35 1.335193e-12 1.486515e-11 1.005136e-04 1.0000000 1.0000000
Gene23 7.562101e-10 6.314354e-09 8.490221e-04 1.0000000 1.0000000
Gene93 1.639168e-03 4.802476e-03 1.027727e+00 0.9845394 1.0000000
Gene166 8.905409e-07 4.131120e-06 1.187855e-02 0.9999824 1.0000000
Gene4 4.225846e-08 2.352388e-07 2.283942e+00 0.8918212 1.0000000
Gene31 5.569724e-07 2.657554e-06 1.677464e+00 0.9468478 1.0000000
Gene19 3.299192e-14 6.121834e-13 7.196461e-04 1.0000000 1.0000000
Gene37 6.667383e-09 4.282512e-08 2.388357e-01 0.9997404 1.0000000
Gene10 9.543653e-05 3.391043e-04 1.908822e-04 0.9999046 1.0000000
Gene34 1.431199e-14 2.987627e-13 1.971146e-02 0.9999998 1.0000000
Gene42 2.872760e-09 2.180686e-08 2.106833e-01 0.9998199 1.0000000
Gene25 1.753789e-04 6.101726e-04 8.916588e-02 0.9999857 1.0000000
Gene30 5.034678e-09 3.503297e-08 1.572375e-01 0.9999236 1.0000000
Gene33 3.832244e-08 2.206844e-07 1.217543e-02 1.0000000 1.0000000
Gene135 5.876027e-04 1.887109e-03 4.204237e-01 0.9986765 1.0000000
Gene1 4.613445e-04 1.540891e-03 3.866447e-02 0.9998155 1.0000000
Gene114 9.733721e-07 4.393328e-06 2.547132e+00 0.6362164 1.0000000
Gene158 1.149163e-03 3.553893e-03 2.284344e+00 0.8917793 1.0000000
Gene40 2.169930e-07 1.098116e-06 7.341502e-01 0.9937242 1.0000000
Gene118 1.111000e-07 5.798033e-07 3.971867e+00 0.4098266 0.7690004
Gene39 1.242866e-09 9.883743e-09 9.921372e-02 0.9988095 1.0000000
Gene28 6.715876e-18 2.803878e-16 2.377650e-04 1.0000000 1.0000000
Gene22 2.735221e-03 7.613031e-03 1.261746e+00 0.9737251 1.0000000
$neg
effectSize effectSizeStandardError effectSizePval effectSizeFDR
Gene65 -0.9108702 0.11697029 6.851455e-15 2.860483e-13
Gene66 -0.5641520 0.07321384 1.302928e-14 4.351779e-13
Gene62 -0.7748318 0.10188377 2.847801e-14 7.926378e-13
Gene59 -0.5772361 0.08198619 1.913453e-12 3.550518e-11
Gene56 -0.4108498 0.06196003 3.336834e-11 4.643760e-10
Gene63 -0.3524544 0.05374244 5.445590e-11 6.995489e-10
Gene50 -0.5383657 0.08423914 1.648892e-10 1.835766e-09
Gene47 -1.0183475 0.18329790 2.765069e-08 2.308833e-07
Gene45 -0.7541341 0.13695479 3.661516e-08 2.911777e-07
Gene49 -0.4418702 0.08307571 1.044044e-07 7.264804e-07
Gene44 -0.5543407 0.10655823 1.969085e-07 1.315349e-06
Gene54 -0.4100211 0.08539501 1.575098e-06 8.768044e-06
Gene94 -0.2384120 0.05366514 8.888416e-06 4.788276e-05
Gene48 -0.8574953 0.20652024 3.294202e-05 1.618035e-04
Gene61 -0.2708759 0.06990700 1.067109e-04 4.816413e-04
Gene53 -0.3364151 0.09560700 4.336198e-04 1.684058e-03
Gene55 -0.6013534 0.17249691 4.899908e-04 1.752801e-03
Gene67 -0.3553792 0.10199248 4.933032e-04 1.752801e-03
Gene51 -0.5241454 0.15231843 5.793205e-04 1.934931e-03
Gene64 -0.5057346 0.14967960 7.280804e-04 2.338258e-03
Gene46 -0.6010021 0.17889758 7.809045e-04 2.460586e-03
Gene52 -0.4259713 0.13418501 1.500909e-03 4.641700e-03
Gene123 -0.2227457 0.07203590 1.987131e-03 5.925908e-03
tauSquared numStudies cochranesQ heterogeneityPval fisherStatUp
Gene65 0.000000000 2 0.06991577 0.79145946 1.882666e-03
Gene66 0.000000000 3 1.29765174 0.52265909 1.724807e+00
Gene62 0.000000000 3 0.73083855 0.69390565 8.455370e-02
Gene59 0.001354013 3 2.11946254 0.34654893 4.061699e-01
Gene56 0.000000000 3 0.16113556 0.92259237 1.225478e+01
Gene63 0.000000000 3 0.06741452 0.96685450 5.384946e+00
Gene50 0.000000000 3 0.01140394 0.99431425 3.306203e+00
Gene47 0.034872885 3 2.98058253 0.22530702 9.530614e-03
Gene45 0.000000000 3 1.85391891 0.39575519 2.094468e-01
Gene49 0.000000000 3 0.66566962 0.71688861 1.319780e+00
Gene44 0.000000000 3 0.01612983 0.99196752 2.257258e-01
Gene54 0.004890694 3 2.40751805 0.30006414 6.224064e+00
Gene94 0.000000000 3 0.23544594 0.88894228 1.582510e+01
Gene48 0.060165779 3 3.70556346 0.15680038 1.851266e-03
Gene61 0.000000000 3 0.08418243 0.95878232 4.167637e+00
Gene53 0.006424830 3 2.43830766 0.29548009 2.600142e+00
Gene55 NA 1 NA NA 4.650652e-04
Gene67 0.005248733 3 2.27453415 0.32069426 2.845783e+00
Gene51 0.038950780 3 4.61057118 0.09973031 4.096826e+00
Gene64 0.035537111 3 4.28700516 0.11724347 1.658011e+00
Gene46 0.043985144 3 3.49979348 0.17379189 2.995090e-01
Gene52 0.000000000 3 0.12417687 0.93979977 3.019494e-01
Gene123 0.000000000 3 0.13812441 0.93326863 4.624696e+00
fisherPvalUp fisherFDRUp fisherStatDown fisherPvalDown fisherFDRDown
Gene65 0.99999956 1.00000000 57.67330 8.936165e-12 3.730849e-10
Gene66 0.94319010 1.00000000 45.26015 4.154898e-08 7.709644e-07
Gene62 0.99998780 1.00000000 50.38042 3.943775e-09 1.097684e-07
Gene59 0.99880030 1.00000000 42.66136 1.360968e-07 1.623441e-06
Gene56 0.05652052 0.13294264 80.04266 3.501101e-15 5.846838e-13
Gene63 0.49547010 0.75126436 42.77509 1.292275e-07 1.623441e-06
Gene50 0.76954907 0.96627590 48.97484 7.542890e-09 1.574578e-07
Gene47 0.99999998 1.00000000 68.42147 8.612657e-13 5.479374e-11
Gene45 0.99982301 1.00000000 44.70639 5.352895e-08 8.126668e-07
Gene49 0.97055581 1.00000000 29.09835 5.828432e-05 3.604993e-04
Gene44 0.99977979 1.00000000 40.33075 3.921747e-07 4.093323e-06
Gene54 0.39856430 0.66560238 68.13827 9.843187e-13 5.479374e-11
Gene94 0.01472418 0.03782983 28.37235 7.994089e-05 4.450043e-04
Gene48 1.00000000 1.00000000 49.35643 6.326239e-09 1.509260e-07
Gene61 0.65400217 0.86575799 28.42636 7.808666e-05 4.450043e-04
Gene53 0.85709619 0.99491018 33.37729 8.870716e-06 7.407048e-05
Gene55 0.99976749 1.00000000 16.73319 2.325055e-04 1.210977e-03
Gene67 0.82793888 0.99471793 26.80175 1.577287e-04 8.496998e-04
Gene51 0.66357498 0.86575799 51.90828 1.945708e-09 6.498665e-08
Gene64 0.94831664 1.00000000 44.90487 4.888401e-08 8.126668e-07
Gene46 0.99949951 1.00000000 42.75611 1.303499e-07 1.623441e-06
Gene52 0.99948764 1.00000000 20.49784 2.257149e-03 9.912288e-03
Gene123 0.59276699 0.80481371 32.54177 1.284392e-05 1.013635e-04
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