Calculate the eigengene of a module from a data set
eigengene.RdCalculate the eigengene of a module from a data set
Arguments
- x
data; genes in rows, samples in columns
- g
genes -- a vector gene IDs corresponding to annotation in modules
- mset
-- a module set; eigengenes will be calculated for each module in the set
- k
which component defines the eigengene (default: 1)
Value
A numeric matrix with rows corresponding to modules. If there was not a sufficient number of genes in a module corresponding to the data set, the row will contain only NA's.
Details
The eigengene of a module is here defined as the first principal component of a PCA on the gene expression of all genes from a module.
Examples
data(Egambia)
data(tmod)
x <- Egambia[ , -c(1:3) ]
ifns <- tmod[ grep("[Ii]nterferon", tmod$gs$Title) ]
eigv <- eigengene(x, Egambia$GENE_SYMBOL, ifns)
plot(eigv["LI.M127", ], eigv["DC.M1.2",])
# which interferon modules are correlated
cor(eigv)
#> NID NID.1 NID.2 NID.3 NID.4 NID.5
#> NID 1.0000000 0.7340461 0.77798648 0.43569182 0.6926534 -1.734962e-01
#> NID.1 0.7340461 1.0000000 0.95401316 0.83478049 0.7306611 2.306428e-01
#> NID.2 0.7779865 0.9540132 1.00000000 0.74323177 0.6722409 -5.528967e-02
#> NID.3 0.4356918 0.8347805 0.74323177 1.00000000 0.8401116 3.873480e-01
#> NID.4 0.6926534 0.7306611 0.67224089 0.84011165 1.0000000 2.541241e-01
#> NID.5 -0.1734962 0.2306428 -0.05528967 0.38734803 0.2541241 1.000000e+00
#> NID.6 0.8756612 0.9478450 0.94194598 0.80322636 0.8452683 5.833721e-02
#> NID.7 0.9548356 0.8843013 0.89828262 0.67475455 0.8236078 -2.060135e-02
#> NID.8 -0.4810708 -0.7120692 -0.56315144 -0.60601374 -0.4078260 -3.478841e-01
#> NID.9 0.6380659 0.5662710 0.60627916 0.07841018 0.1981659 4.324869e-05
#> NID.10 0.8403301 0.7763935 0.74094404 0.77326055 0.9276373 7.791330e-02
#> NID.11 -0.3180777 -0.7121303 -0.61548802 -0.96721064 -0.7734526 -3.454134e-01
#> NID.12 0.7737778 0.9495713 0.98561371 0.82191750 0.7683774 -3.091130e-02
#> NID.13 0.9099939 0.8284390 0.78934672 0.58557580 0.7976842 1.917862e-01
#> NID.14 -0.1343416 -0.2774313 -0.20654154 -0.69664252 -0.6533970 -1.571156e-01
#> TB -0.6544796 -0.5961499 -0.63533955 -0.11489311 -0.2276562 -4.990075e-03
#> TB.1 -0.3304879 -0.1769852 -0.15061192 -0.41894723 -0.7644742 -1.999860e-01
#> TB.2 -0.2341156 -0.4330071 -0.60783939 -0.10169786 0.1298679 4.313480e-01
#> TB.3 -0.6537368 -0.8475219 -0.83803820 -0.92962662 -0.8770582 -6.571663e-02
#> TB.4 -0.7060308 -0.4003332 -0.62168527 -0.26606706 -0.4737239 7.183756e-01
#> TB.5 -0.2839792 -0.3754146 -0.46711297 0.09143206 0.1653776 1.280893e-01
#> TB.6 0.6600716 0.8701071 0.88239264 0.86625597 0.7391022 -3.975092e-02
#> TB.7 -0.7966635 -0.9786370 -0.96792652 -0.73416627 -0.6975659 -1.405127e-01
#> TB.8 -0.8829098 -0.9458024 -0.94452731 -0.64804464 -0.6881623 -7.347971e-02
#> TB.9 -0.7693677 -0.9855857 -0.95954455 -0.73275699 -0.6364853 -1.506282e-01
#> TB.10 0.3578804 0.5199361 0.67276398 0.13671390 -0.0866007 -4.152575e-01
#> TB.11 -0.1857347 -0.1500524 0.09807492 -0.33949876 -0.4906118 -6.787103e-01
#> TB.12 -0.8189205 -0.9295643 -0.92003603 -0.60836887 -0.6271554 -1.396041e-01
#> TB.13 -0.8518470 -0.9525634 -0.95482739 -0.68567649 -0.7170650 -9.502084e-02
#> TB.14 -0.8337039 -0.9781274 -0.97603940 -0.80233886 -0.7764050 -6.419038e-02
#> NID.6 NID.7 NID.8 NID.9 NID.10
#> NID 0.87566122 0.95483555 -0.48107084 6.380659e-01 0.84033007
#> NID.1 0.94784501 0.88430128 -0.71206920 5.662710e-01 0.77639351
#> NID.2 0.94194598 0.89828262 -0.56315144 6.062792e-01 0.74094404
#> NID.3 0.80322636 0.67475455 -0.60601374 7.841018e-02 0.77326055
#> NID.4 0.84526830 0.82360783 -0.40782595 1.981659e-01 0.92763729
#> NID.5 0.05833721 -0.02060135 -0.34788413 4.324869e-05 0.07791330
#> NID.6 1.00000000 0.97704511 -0.64401417 5.097922e-01 0.91720401
#> NID.7 0.97704511 1.00000000 -0.56294339 5.953459e-01 0.91157034
#> NID.8 -0.64401417 -0.56294339 1.00000000 -1.585251e-01 -0.61122011
#> NID.9 0.50979223 0.59534595 -0.15852505 1.000000e+00 0.23157490
#> NID.10 0.91720401 0.91157034 -0.61122011 2.315749e-01 1.00000000
#> NID.11 -0.69957799 -0.55325071 0.62610321 1.571175e-01 -0.73673533
#> NID.12 0.96541657 0.91190778 -0.56669163 4.917367e-01 0.81826656
#> NID.13 0.89114042 0.94192214 -0.47450406 7.190426e-01 0.81857892
#> NID.14 -0.39157910 -0.28581938 0.37648308 5.778862e-01 -0.63154589
#> TB -0.53981271 -0.62026756 0.18012972 -9.992731e-01 -0.26056218
#> TB.1 -0.35239539 -0.39428864 -0.21716936 1.480823e-02 -0.54288263
#> TB.2 -0.31466633 -0.28022823 0.06586720 -5.766755e-01 0.05021625
#> TB.3 -0.90833069 -0.82391276 0.59882562 -1.345957e-01 -0.90215713
#> TB.4 -0.60963802 -0.66513646 0.02363313 -2.726630e-01 -0.59265792
#> TB.5 -0.22914673 -0.26810816 -0.01678149 -8.784607e-01 0.14656595
#> TB.6 0.90237277 0.81103279 -0.69772482 1.812551e-01 0.84197903
#> TB.7 -0.94130149 -0.91228883 0.60021618 -7.085946e-01 -0.73854320
#> TB.8 -0.94552686 -0.94996228 0.60177810 -7.532665e-01 -0.76828095
#> TB.9 -0.92869877 -0.88413287 0.71494136 -6.592636e-01 -0.72399710
#> TB.10 0.41170699 0.38371956 -0.24820743 6.162657e-01 0.06072030
#> TB.11 -0.20901503 -0.20955715 0.46996776 2.175370e-01 -0.47336749
#> TB.12 -0.89111800 -0.89484329 0.54041102 -8.241310e-01 -0.67144924
#> TB.13 -0.94525855 -0.94108352 0.54722048 -7.476153e-01 -0.75913704
#> TB.14 -0.98866788 -0.95021228 0.66457734 -5.564392e-01 -0.85165175
#> NID.11 NID.12 NID.13 NID.14 TB
#> NID -0.31807767 0.773777840 0.9099939 -0.13434156 -0.654479590
#> NID.1 -0.71213029 0.949571293 0.8284390 -0.27743134 -0.596149920
#> NID.2 -0.61548802 0.985613714 0.7893467 -0.20654154 -0.635339553
#> NID.3 -0.96721064 0.821917503 0.5855758 -0.69664252 -0.114893112
#> NID.4 -0.77345256 0.768377430 0.7976842 -0.65339702 -0.227656219
#> NID.5 -0.34541337 -0.030911302 0.1917862 -0.15711564 -0.004990075
#> NID.6 -0.69957799 0.965416567 0.8911404 -0.39157910 -0.539812707
#> NID.7 -0.55325071 0.911907781 0.9419221 -0.28581938 -0.620267563
#> NID.8 0.62610321 -0.566691632 -0.4745041 0.37648308 0.180129718
#> NID.9 0.15711754 0.491736690 0.7190426 0.57788617 -0.999273111
#> NID.10 -0.73673533 0.818266556 0.8185789 -0.63154589 -0.260562184
#> NID.11 1.00000000 -0.717113060 -0.4160525 0.83369527 -0.120462002
#> NID.12 -0.71711306 1.000000000 0.7870787 -0.36138921 -0.523961175
#> NID.13 -0.41605250 0.787078745 1.0000000 -0.11730749 -0.737154188
#> NID.14 0.83369527 -0.361389210 -0.1173075 1.00000000 -0.549375803
#> TB -0.12046200 -0.523961175 -0.7371542 -0.54937580 1.000000000
#> TB.1 0.36165203 -0.265623092 -0.4756171 0.48350122 -0.002285465
#> TB.2 -0.01720856 -0.499936438 -0.1640475 -0.41370097 0.584867685
#> TB.3 0.90574639 -0.915949390 -0.6643777 0.70423756 0.171254936
#> TB.4 0.22769184 -0.646727640 -0.4622499 0.23229497 0.289579675
#> TB.5 -0.30060329 -0.320490564 -0.3482806 -0.75150895 0.873606287
#> TB.6 -0.85202294 0.931489381 0.6102478 -0.60666554 -0.216909522
#> TB.7 0.57450973 -0.943522533 -0.8823073 0.12463608 0.734570474
#> TB.8 0.48707671 -0.914920286 -0.9268414 0.07785277 0.776066388
#> TB.9 0.59816723 -0.930089598 -0.8293954 0.14347513 0.685648607
#> TB.10 -0.02647334 0.561375851 0.2541044 0.38031162 -0.625688853
#> TB.11 0.39000033 0.007723622 -0.3231090 0.51245393 -0.211287698
#> TB.12 0.42082046 -0.873608565 -0.9116563 -0.03823067 0.844385571
#> TB.13 0.51603308 -0.930561213 -0.9239908 0.09427945 0.771666476
#> TB.14 0.68874472 -0.981648585 -0.8603866 0.31898318 0.586545117
#> TB.1 TB.2 TB.3 TB.4 TB.5 TB.6
#> NID -0.330487895 -0.23411559 -0.65373682 -0.70603081 -0.28397915 0.66007162
#> NID.1 -0.176985180 -0.43300715 -0.84752192 -0.40033317 -0.37541455 0.87010714
#> NID.2 -0.150611919 -0.60783939 -0.83803820 -0.62168527 -0.46711297 0.88239264
#> NID.3 -0.418947227 -0.10169786 -0.92962662 -0.26606706 0.09143206 0.86625597
#> NID.4 -0.764474179 0.12986795 -0.87705823 -0.47372390 0.16537761 0.73910216
#> NID.5 -0.199985996 0.43134804 -0.06571663 0.71837563 0.12808933 -0.03975092
#> NID.6 -0.352395392 -0.31466633 -0.90833069 -0.60963802 -0.22914673 0.90237277
#> NID.7 -0.394288638 -0.28022823 -0.82391276 -0.66513646 -0.26810816 0.81103279
#> NID.8 -0.217169363 0.06586720 0.59882562 0.02363313 -0.01678149 -0.69772482
#> NID.9 0.014808230 -0.57667549 -0.13459572 -0.27266296 -0.87846074 0.18125508
#> NID.10 -0.542882627 0.05021625 -0.90215713 -0.59265792 0.14656595 0.84197903
#> NID.11 0.361652030 -0.01720856 0.90574639 0.22769184 -0.30060329 -0.85202294
#> NID.12 -0.265623092 -0.49993644 -0.91594939 -0.64672764 -0.32049056 0.93148938
#> NID.13 -0.475617122 -0.16404751 -0.66437774 -0.46224989 -0.34828058 0.61024777
#> NID.14 0.483501220 -0.41370097 0.70423756 0.23229497 -0.75150895 -0.60666554
#> TB -0.002285465 0.58486769 0.17125494 0.28957967 0.87360629 -0.21690952
#> TB.1 1.000000000 -0.44409891 0.42355047 0.29808958 -0.33967090 -0.18270269
#> TB.2 -0.444098908 1.00000000 0.18700992 0.42092095 0.81772264 -0.34718704
#> TB.3 0.423550473 0.18700992 1.00000000 0.58059746 -0.08041998 -0.96569126
#> TB.4 0.298089581 0.42092095 0.58059746 1.00000000 0.14279440 -0.59903621
#> TB.5 -0.339670904 0.81772264 -0.08041998 0.14279440 1.00000000 -0.02900436
#> TB.6 -0.182702687 -0.34718704 -0.96569126 -0.59903621 -0.02900436 1.00000000
#> TB.7 0.196048777 0.51142297 0.77754307 0.47129975 0.51247495 -0.79934897
#> TB.8 0.199571885 0.46824105 0.73681984 0.52301158 0.50926668 -0.76401158
#> TB.9 0.062721103 0.51946374 0.77407446 0.42119081 0.48536009 -0.82984952
#> TB.10 0.503440922 -0.97573435 -0.24961886 -0.44293758 -0.80152033 0.43540358
#> TB.11 0.435622227 -0.80500976 0.23636108 -0.32792620 -0.58783844 -0.11105102
#> TB.12 0.172474604 0.51453056 0.65671273 0.43286798 0.61301882 -0.68078601
#> TB.13 0.256536168 0.48220801 0.75569266 0.52302291 0.51706377 -0.76543984
#> TB.14 0.243177777 0.42927180 0.88781960 0.57240936 0.33119533 -0.90761097
#> TB.7 TB.8 TB.9 TB.10 TB.11 TB.12
#> NID -0.79666351 -0.88290982 -0.76936770 0.35788036 -0.185734668 -0.81892047
#> NID.1 -0.97863701 -0.94580240 -0.98558567 0.51993611 -0.150052382 -0.92956430
#> NID.2 -0.96792652 -0.94452731 -0.95954455 0.67276398 0.098074922 -0.92003603
#> NID.3 -0.73416627 -0.64804464 -0.73275699 0.13671390 -0.339498760 -0.60836887
#> NID.4 -0.69756595 -0.68816227 -0.63648533 -0.08660070 -0.490611839 -0.62715543
#> NID.5 -0.14051273 -0.07347971 -0.15062819 -0.41525754 -0.678710349 -0.13960414
#> NID.6 -0.94130149 -0.94552686 -0.92869877 0.41170699 -0.209015031 -0.89111800
#> NID.7 -0.91228883 -0.94996228 -0.88413287 0.38371956 -0.209557152 -0.89484329
#> NID.8 0.60021618 0.60177810 0.71494136 -0.24820743 0.469967764 0.54041102
#> NID.9 -0.70859461 -0.75326646 -0.65926358 0.61626571 0.217537045 -0.82413104
#> NID.10 -0.73854320 -0.76828095 -0.72399710 0.06072030 -0.473367493 -0.67144924
#> NID.11 0.57450973 0.48707671 0.59816723 -0.02647334 0.390000328 0.42082046
#> NID.12 -0.94352253 -0.91492029 -0.93008960 0.56137585 0.007723622 -0.87360856
#> NID.13 -0.88230734 -0.92684139 -0.82939544 0.25410440 -0.323108950 -0.91165632
#> NID.14 0.12463608 0.07785277 0.14347513 0.38031162 0.512453932 -0.03823067
#> TB 0.73457047 0.77606639 0.68564861 -0.62568885 -0.211287698 0.84438557
#> TB.1 0.19604878 0.19957189 0.06272110 0.50344092 0.435622227 0.17247460
#> TB.2 0.51142297 0.46824105 0.51946374 -0.97573435 -0.805009763 0.51453056
#> TB.3 0.77754307 0.73681984 0.77407446 -0.24961886 0.236361081 0.65671273
#> TB.4 0.47129975 0.52301158 0.42119081 -0.44293758 -0.327926197 0.43286798
#> TB.5 0.51247495 0.50926668 0.48536009 -0.80152033 -0.587838436 0.61301882
#> TB.6 -0.79934897 -0.76401158 -0.82984952 0.43540358 -0.111051022 -0.68078601
#> TB.7 1.00000000 0.98426163 0.98489508 -0.58680560 0.048731754 0.98164190
#> TB.8 0.98426163 1.00000000 0.96895130 -0.56513568 0.084735154 0.98630687
#> TB.9 0.98489508 0.96895130 1.00000000 -0.61944375 0.069527590 0.95741472
#> TB.10 -0.58680560 -0.56513568 -0.61944375 1.00000000 0.696897059 -0.59236549
#> TB.11 0.04873175 0.08473515 0.06952759 0.69689706 1.000000000 0.03399204
#> TB.12 0.98164190 0.98630687 0.95741472 -0.59236549 0.033992037 1.00000000
#> TB.13 0.99242123 0.99385347 0.96405792 -0.55795686 0.057476994 0.98837873
#> TB.14 0.97204537 0.96206201 0.96901144 -0.52149131 0.117519234 0.92206173
#> TB.13 TB.14
#> NID -0.85184701 -0.83370395
#> NID.1 -0.95256337 -0.97812735
#> NID.2 -0.95482739 -0.97603940
#> NID.3 -0.68567649 -0.80233886
#> NID.4 -0.71706500 -0.77640500
#> NID.5 -0.09502084 -0.06419038
#> NID.6 -0.94525855 -0.98866788
#> NID.7 -0.94108352 -0.95021228
#> NID.8 0.54722048 0.66457734
#> NID.9 -0.74761532 -0.55643916
#> NID.10 -0.75913704 -0.85165175
#> NID.11 0.51603308 0.68874472
#> NID.12 -0.93056121 -0.98164859
#> NID.13 -0.92399082 -0.86038663
#> NID.14 0.09427945 0.31898318
#> TB 0.77166648 0.58654512
#> TB.1 0.25653617 0.24317778
#> TB.2 0.48220801 0.42927180
#> TB.3 0.75569266 0.88781960
#> TB.4 0.52302291 0.57240936
#> TB.5 0.51706377 0.33119533
#> TB.6 -0.76543984 -0.90761097
#> TB.7 0.99242123 0.97204537
#> TB.8 0.99385347 0.96206201
#> TB.9 0.96405792 0.96901144
#> TB.10 -0.55795686 -0.52149131
#> TB.11 0.05747699 0.11751923
#> TB.12 0.98837873 0.92206173
#> TB.13 1.00000000 0.96366110
#> TB.14 0.96366110 1.00000000