batchqc_pca: Performs principal component analysis and produces plot of...
In BatchQC: Batch Effects Quality Control Software
Description
Usage
Arguments
Value
Examples
Description
Performs principal component analysis and
produces plot of the first two principal components
Usage
1
batchqc_pca(data.matrix, batch, mod = NULL)
Arguments
data.matrix
Given data or simulated data from rnaseq_sim()
batch
Batch covariate
mod
Model matrix for outcome of interest and other covariates
besides batch
Value
PCA object from principal component analysis
Examples
1
2
3
4
5
6
7
8
9
10
11
nbatch <- 3
ncond <- 2
npercond <- 10
data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800,
basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
batch <- rep(1:nbatch, each=ncond*npercond)
condition <- rep(rep(1:ncond, each=npercond), nbatch)
pdata <- data.frame(batch, condition)
modmatrix = model.matrix(~as.factor(condition), data=pdata)
batchqc_pca(data.matrix, batch, mod=modmatrix)
Example output
sh: 1: cannot create /dev/null: Permission denied
Standard deviations (1, .., p=50):
[1] 5.37385516 1.24203430 1.20861596 1.14822039 1.07868428 1.04344750
[7] 0.98556583 0.97947654 0.92174077 0.91320945 0.89449780 0.86149785
[13] 0.84706775 0.82180281 0.78228239 0.76482753 0.74616903 0.72621231
[19] 0.68668468 0.67677100 0.65945857 0.63172156 0.62143893 0.57437768
[25] 0.55426563 0.54913491 0.51748897 0.50242423 0.49012697 0.47951732
[31] 0.46361561 0.42724253 0.41669333 0.38607166 0.36938047 0.34214576
[37] 0.31700973 0.29762569 0.28727510 0.28553312 0.25856150 0.24807391
[43] 0.21978999 0.17624031 0.16927586 0.15770845 0.14164507 0.11290626
[49] 0.10481578 0.07966933
Rotation (n x k) = (50 x 50):
PC1 PC2 PC3 PC4 PC5
[1,] 0.1428409 0.093906004 -0.09708496 0.098095278 -0.138884700
[2,] 0.1432312 -0.052758087 0.10416026 -0.014042349 0.049685604
[3,] 0.1365965 0.165763489 -0.16000022 0.098825776 -0.028820049
[4,] 0.1469878 -0.219091929 -0.04951724 -0.049684634 -0.047872749
[5,] 0.1432096 -0.047711504 -0.14473273 0.099669617 0.240824830
[6,] 0.1491981 0.070114109 0.01425394 0.079000459 -0.080750203
[7,] 0.1429338 0.132072602 -0.13705556 -0.050849739 -0.268729888
[8,] 0.1413007 0.069892777 -0.13885508 -0.108566261 0.264297425
[9,] 0.1463438 0.114626327 -0.26323460 0.008684241 -0.018485553
[10,] 0.1422389 -0.115896459 0.16688856 0.232385695 -0.143539494
[11,] 0.1372982 0.052880496 -0.07533488 -0.245358373 -0.207851109
[12,] 0.1379562 0.281255568 -0.04395646 0.144068813 -0.138330061
[13,] 0.1562253 0.119421687 0.07530289 -0.001775128 -0.016220709
[14,] 0.1361448 -0.135401686 0.20449879 0.158073402 0.187053235
[15,] 0.1454618 -0.248680002 0.16810132 0.036362378 0.017525777
[16,] 0.1494762 -0.107087833 -0.05799968 -0.155035063 0.027386310
[17,] 0.1451022 0.007961209 -0.18004497 0.005023514 0.051043323
[18,] 0.1282341 0.067293859 0.18149589 0.133104571 -0.229307603
[19,] 0.1418664 0.096316720 0.12728688 -0.014562895 -0.060107723
[20,] 0.1435351 0.189613624 0.02165129 0.152963057 0.168530308
[21,] 0.1556216 -0.099733483 -0.02627934 0.095822646 0.070996725
[22,] 0.1421520 -0.060135279 -0.17786720 -0.009941430 -0.166750425
[23,] 0.1368131 -0.168287016 -0.15896895 0.135336377 -0.141469857
[24,] 0.1454848 0.054482141 0.03939914 0.007426360 0.033462094
[25,] 0.1430666 -0.215989251 0.05196058 0.008788797 -0.112062597
[26,] 0.1407790 0.060908760 0.08991103 -0.184375825 0.074989542
[27,] 0.1514542 0.064435824 0.11010495 -0.128734611 -0.006757529
[28,] 0.1507267 -0.011617560 0.03129210 0.142512895 -0.127936950
[29,] 0.1471663 -0.212554490 0.14865359 -0.172602057 0.081994068
[30,] 0.1471254 0.146392440 -0.09911845 -0.132005666 0.034106696
[31,] 0.1355319 -0.157483834 0.12896004 -0.174241666 -0.130450890
[32,] 0.1434191 -0.010340115 -0.09677506 -0.094957364 0.014614964
[33,] 0.1458222 0.111118905 0.08458383 -0.016327089 0.085994647
[34,] 0.1417662 0.086506607 0.11232353 0.097662109 -0.387748104
[35,] 0.1447757 -0.252323247 0.12837721 0.188582955 0.071448301
[36,] 0.1397404 0.075581682 -0.02735131 -0.114777168 0.331256033
[37,] 0.1467416 0.214076244 0.04413713 0.092506613 0.209168072
[38,] 0.1288961 -0.303234776 -0.27240707 -0.065597009 0.089669429
[39,] 0.1333704 0.055220390 -0.16339313 0.246453943 -0.056409530
[40,] 0.1277452 -0.018300443 0.19110456 -0.049596150 0.026956740
[41,] 0.1261049 0.170624260 0.21726570 0.002551940 -0.079841560
[42,] 0.1335246 -0.002956071 0.24980722 0.241166323 0.199570562
[43,] 0.1449802 0.005032074 -0.04969729 -0.109199793 -0.016729685
[44,] 0.1333428 -0.269422953 0.01371882 -0.211486353 -0.156053862
[45,] 0.1323319 -0.213015485 -0.17435643 0.268533572 0.118758829
[46,] 0.1408328 0.035752536 -0.27653977 0.014759087 0.094089757
[47,] 0.1477849 0.070302812 -0.15680312 0.000778323 0.008954019
[48,] 0.1317724 0.143787614 0.13147013 -0.240469883 0.092266259
[49,] 0.1330103 -0.002890743 0.01845944 -0.389578225 -0.031174549
[50,] 0.1344629 0.154246751 0.21882797 -0.064156759 0.128102550
PC6 PC7 PC8 PC9 PC10
[1,] 1.057742e-01 -0.23538711 0.08386086 -0.042490448 0.106228703
[2,] 2.127898e-01 0.02892399 -0.07926812 -0.250263525 0.128446951
[3,] 2.915453e-01 0.23986862 0.01281772 0.241629294 -0.086788332
[4,] -8.877456e-03 0.06829730 0.19116250 0.266930310 -0.171680549
[5,] 7.478338e-02 -0.26904163 -0.13087882 -0.040797907 -0.004268275
[6,] 4.594550e-02 -0.00674125 0.16469339 0.099466542 0.023100654
[7,] -3.844750e-02 -0.17287273 -0.06680536 -0.019570467 0.202173661
[8,] -1.061109e-01 0.08911107 0.16578011 0.069245467 -0.055583334
[9,] 9.192449e-02 0.03184259 0.02780395 0.034390274 0.091813904
[10,] 8.516620e-02 -0.07790053 -0.28680431 -0.051243173 -0.126625608
[11,] -6.885604e-02 -0.10085691 0.14607128 -0.306814459 0.004118581
[12,] -1.347301e-02 0.10634248 -0.26411606 -0.031665758 -0.187959973
[13,] -2.065483e-01 -0.07175860 -0.06654491 0.030032905 0.061641044
[14,] 1.139226e-01 -0.01508137 0.09877166 0.239035719 0.085366149
[15,] 3.732541e-02 -0.05038467 0.10585356 0.101664049 -0.113483885
[16,] 2.064711e-02 0.19422998 0.10009077 -0.240337269 0.124151802
[17,] -2.489234e-01 0.15787775 -0.07613443 0.045882382 -0.013287985
[18,] -6.252651e-02 0.28965305 -0.26479355 0.134276256 0.067522482
[19,] -2.480382e-01 0.09791055 -0.11286878 0.032776989 0.198625081
[20,] 8.555796e-02 -0.04894219 -0.04787438 -0.104269659 0.189706624
[21,] -7.427736e-02 -0.03287849 0.23703666 -0.087858106 -0.161902588
[22,] -1.366387e-01 -0.08797062 -0.00150032 -0.009268987 -0.273208280
[23,] 1.156844e-01 -0.15023829 0.01017285 -0.088249286 -0.274122658
[24,] 1.887317e-01 0.09539473 0.16957954 0.027121172 0.301054245
[25,] 8.541816e-02 0.01305351 -0.14683465 0.254814297 0.039812151
[26,] 2.173556e-01 0.02062515 0.07578603 0.073635706 0.144239958
[27,] -9.440647e-02 -0.01892817 -0.09871189 -0.005641399 0.092442767
[28,] -9.183493e-05 0.06420247 0.09825811 -0.134786778 0.123207516
[29,] -1.487517e-01 0.04400108 -0.18710875 -0.053331849 0.173039351
[30,] 2.993303e-02 -0.16141993 -0.23577764 0.055983477 -0.036798606
[31,] 2.351830e-01 -0.21617188 -0.01983191 0.102927026 -0.029330750
[32,] 1.527496e-01 0.08609514 -0.16058057 -0.302782433 -0.026317495
[33,] 1.055833e-01 0.02958946 0.12841874 -0.085310656 0.126258415
[34,] -3.569113e-02 -0.01307430 0.16640043 -0.006521833 -0.082445301
[35,] 3.877703e-02 -0.07254960 0.15238727 -0.081458103 0.059246335
[36,] -6.812919e-02 0.03331068 -0.07354879 0.012493903 -0.139407213
[37,] -3.364137e-02 -0.06260033 0.18797769 0.031059751 -0.015924459
[38,] -2.283315e-01 -0.02056102 -0.13650870 0.059176147 0.045051991
[39,] -4.151309e-02 0.22920349 0.26342216 -0.110908262 -0.014999874
[40,] -2.519362e-01 -0.37118844 -0.00772624 -0.134642861 0.067441271
[41,] -3.579160e-01 -0.09643413 0.22688946 0.192797728 -0.035642121
[42,] 1.046422e-01 0.02813609 -0.12721625 -0.268383534 -0.238935158
[43,] -5.078433e-02 0.22231466 -0.02449162 -0.189289478 -0.061919470
[44,] 1.043704e-02 0.17861668 0.05556456 0.033439927 0.122353139
[45,] -2.339735e-01 0.19485836 -0.09112715 -0.022423759 0.045502871
[46,] 3.200647e-03 -0.21737615 -0.02807754 0.188034776 0.180365526
[47,] 1.392410e-01 -0.18910626 -0.11738840 0.186745558 -0.057392465
[48,] -3.346974e-02 -0.01360015 0.11936259 -0.075817863 -0.398787143
[49,] 1.789439e-01 0.14631769 -0.03384321 0.058552166 -0.168043756
[50,] -2.914245e-02 0.11187162 -0.13755855 0.209348365 -0.103254896
PC11 PC12 PC13 PC14 PC15
[1,] -0.001572544 -0.025974715 0.1028527090 0.3169193795 -0.220371867
[2,] 0.014643830 0.043274223 0.0722104070 -0.3829889251 -0.166768453
[3,] -0.199099361 -0.049204534 0.0822500485 -0.0386086957 -0.039800780
[4,] 0.021603322 -0.080032463 -0.1472446124 -0.0405373909 -0.036373310
[5,] -0.015850778 0.003971891 -0.0681253845 -0.1915098471 0.241337770
[6,] 0.222641735 -0.007899558 -0.1489148348 0.1749101128 0.236709533
[7,] 0.117247013 -0.089210452 0.0543867853 0.1833842482 -0.137319301
[8,] -0.071671804 0.313580721 0.1135565313 -0.0070633887 0.092834995
[9,] 0.160369038 0.303356345 -0.0028328523 0.1369204575 -0.048275771
[10,] -0.014256516 0.087717677 0.1308976338 0.1094219388 -0.068769016
[11,] 0.043986909 0.089164222 0.2367615932 -0.1986134162 0.041613226
[12,] -0.017374859 -0.129875698 0.0625206956 -0.0192922172 0.120335359
[13,] -0.008203427 0.162778489 0.0017158134 -0.0359413340 -0.120105043
[14,] 0.082426667 -0.089155072 0.3130974265 -0.1528451949 -0.005074339
[15,] 0.152831640 0.134518601 -0.0344526791 0.0255783119 -0.023442416
[16,] -0.110429020 -0.225027787 0.0182613560 -0.0286327553 0.090045988
[17,] -0.237917016 -0.032582814 0.2835440990 0.0391347922 -0.022352664
[18,] 0.167851224 -0.039418621 -0.0183441492 -0.1625123118 0.282661860
[19,] -0.219801350 -0.135327606 -0.2079683190 -0.0041655854 0.093654346
[20,] 0.056554416 0.098253275 0.1960658842 0.0275989511 0.131165578
[21,] -0.099094943 -0.186857501 0.0351263445 0.0627873355 -0.075657222
[22,] 0.081170897 -0.177309218 -0.0004306734 -0.1408558251 -0.255391879
[23,] -0.254809894 -0.087339937 -0.0871920914 -0.0056519045 0.091742482
[24,] -0.162326589 0.005461561 -0.2149585791 0.0641861884 -0.031553630
[25,] -0.086224482 0.191970488 -0.0314871801 -0.1342883312 -0.038332296
[26,] -0.008089449 -0.378796108 -0.0425453566 0.0365920766 -0.281025765
[27,] 0.384798803 -0.164401803 0.0446148983 0.0737688219 -0.038019601
[28,] 0.163514835 0.193272745 0.1982579990 -0.0007495177 -0.021009069
[29,] -0.078737959 -0.078188548 -0.0565589264 0.0108127341 -0.098782912
[30,] -0.079058730 -0.071328427 -0.2606803223 -0.0598080727 -0.002385048
[31,] 0.070285361 -0.067794005 0.0540622270 0.2566659061 0.350212381
[32,] -0.150899395 -0.001910786 -0.0157900396 0.1274311118 -0.007233154
[33,] -0.091260464 -0.094217689 -0.0174794962 0.0048745461 0.253423106
[34,] 0.020891902 0.106745421 -0.1405932804 0.0060755511 -0.053209651
[35,] 0.045444094 -0.042773903 -0.2009689758 -0.0043969283 0.009883379
[36,] 0.305287332 -0.204306826 0.1092495736 0.0848711852 0.086124225
[37,] -0.084847356 0.086948481 -0.0719572658 0.1764877744 -0.177140577
[38,] 0.146880744 0.074882842 -0.0518253681 0.1269040581 0.022266084
[39,] 0.050958264 0.041803354 -0.1189945153 -0.1854611727 0.143101651
[40,] -0.265727318 0.197137826 -0.0705886900 -0.0169971845 0.146584697
[41,] -0.153885089 -0.186102196 0.1241131592 -0.1019856951 0.067825301
[42,] 0.010242451 0.026182825 -0.0480929292 0.0235309705 -0.145524508
[43,] 0.182509144 0.038061946 -0.3599266531 -0.0797281607 -0.109261402
[44,] -0.061697972 0.115509597 0.2579300845 -0.0863525660 -0.122984110
[45,] -0.041593793 -0.083060492 0.0578308910 0.2988105123 0.030343540
[46,] 0.139060195 0.055819368 -0.1937205812 -0.3230992373 -0.023402058
[47,] -0.106882457 -0.100274480 0.1776645462 -0.1786404359 -0.031874712
[48,] 0.162874000 0.048320452 0.0499793759 -0.0746475432 0.032971397
[49,] -0.149286374 0.183544142 -0.0146956279 0.1779612297 0.209791844
[50,] -0.075741358 0.256123179 -0.1104181284 0.0895923465 -0.286742711
PC16 PC17 PC18 PC19 PC20
[1,] 0.157940786 0.029997504 -0.292465609 0.116430638 0.081323845
[2,] 0.044469208 -0.119015831 -0.014291059 -0.197078579 0.238355940
[3,] 0.078727526 -0.120676517 -0.062934337 0.032209482 0.269020548
[4,] 0.197469349 0.101007167 -0.067287300 0.065479732 -0.148918599
[5,] 0.101845576 -0.132819630 -0.036179960 0.150729456 -0.101538905
[6,] -0.158057265 -0.106833777 0.116158911 -0.123001138 0.086484819
[7,] 0.094961698 -0.293016113 0.202830099 -0.025857567 0.002680321
[8,] 0.100793592 -0.210478210 0.062321154 -0.060203688 -0.154150540
[9,] -0.033171701 0.251658296 -0.077850930 -0.069054593 0.031795454
[10,] -0.055140232 0.007899536 0.083566663 -0.315146759 -0.014189068
[11,] 0.111390406 -0.228296240 -0.042349380 -0.025970333 -0.141372850
[12,] -0.202428168 -0.162070486 -0.147334102 0.062569881 -0.080859865
[13,] 0.117031674 0.277425348 -0.071562592 -0.131925000 0.064835890
[14,] 0.007069339 -0.145547091 0.135915082 0.074453589 0.017458015
[15,] 0.067343136 -0.006582200 -0.136306461 -0.165260211 -0.156044495
[16,] -0.059205484 0.209746381 -0.165922334 0.093568636 -0.118393701
[17,] -0.019773630 0.086682418 -0.127331343 -0.048675822 0.187679957
[18,] 0.078554846 -0.039997840 -0.220578011 0.130852299 -0.109140063
[19,] 0.260366176 0.130715576 0.201397498 -0.183000843 -0.075862230
[20,] -0.176865095 0.270687263 0.106036033 -0.139057148 -0.217257230
[21,] -0.226515229 -0.105910708 0.036661107 -0.015672207 0.065481620
[22,] 0.069318633 0.039599648 0.277675750 0.198756099 -0.241158543
[23,] 0.012231926 -0.063444044 -0.248941922 -0.186833188 0.024968185
[24,] -0.208921914 -0.154284843 -0.146333519 -0.108900264 -0.263114318
[25,] -0.082311944 0.225114188 -0.083158233 0.181093859 -0.199646301
[26,] -0.055880242 0.168893707 -0.034321901 -0.138823126 -0.012896693
[27,] -0.131294543 -0.079744899 -0.231248829 0.054294631 -0.062946475
[28,] 0.228148421 0.190544412 0.058860041 0.126045389 0.155172403
[29,] 0.107142520 -0.171848675 -0.062820016 -0.193854758 0.091109649
[30,] 0.127327761 0.072790835 0.199499575 -0.149693049 0.059875261
[31,] 0.152347118 0.021626345 0.093468668 0.104308872 -0.007098285
[32,] -0.277771167 0.062275182 0.108793211 0.192989095 -0.267321777
[33,] 0.192620111 -0.108353344 -0.060098879 0.253154867 0.247383100
[34,] -0.166046633 -0.029359460 0.148716720 -0.015857986 0.096576370
[35,] -0.153823888 0.130421898 0.084841671 0.062132483 0.228641545
[36,] -0.089415136 0.087654310 0.240154945 0.023399155 0.085966066
[37,] 0.221031920 -0.051699124 -0.036402213 0.112272884 -0.202108616
[38,] -0.219521551 -0.127922824 -0.113295710 -0.084825550 0.215493295
[39,] -0.076179849 0.046022237 0.205187184 -0.142799897 0.029734045
[40,] -0.181758299 0.063396679 -0.026360018 0.257108153 0.139251692
[41,] -0.113743410 0.002060014 -0.007356113 -0.062399015 -0.028709703
[42,] 0.193953205 -0.097288505 0.074376446 0.009824625 -0.106708539
[43,] 0.092023612 0.050116970 -0.012218925 0.271901573 0.195800792
[44,] -0.083941040 -0.068066614 0.171978247 0.096643088 -0.066311941
[45,] 0.176325718 -0.028783676 0.002013910 0.011187741 -0.074683026
[46,] -0.026442812 -0.122666483 -0.067848564 -0.088397064 -0.101760956
[47,] -0.066724912 0.229008587 0.082032888 0.117671040 0.154318064
[48,] 0.006349858 0.156125287 -0.316058765 -0.186276444 0.025429292
[49,] 0.047460310 -0.014420762 0.192157806 -0.155014319 0.064137061
[50,] -0.210781328 -0.209457411 0.028513320 0.227555225 0.093777502
PC21 PC22 PC23 PC24 PC25
[1,] 0.023790050 0.045922678 -0.066189722 -0.1724427896 0.0738057514
[2,] -0.231859444 -0.041088949 -0.159015991 0.0190142393 -0.0404572285
[3,] 0.013426882 -0.092828422 -0.082675676 -0.1878235829 -0.0146970004
[4,] -0.093315341 -0.056007201 0.214795681 -0.0724890454 0.2294171887
[5,] 0.068253551 -0.014221205 0.028167604 -0.2565224685 -0.0782288162
[6,] -0.033162321 0.343095876 -0.170030662 0.3339797410 -0.0713892085
[7,] 0.056127239 0.092656234 0.039403397 -0.0316036192 0.1462774575
[8,] -0.094283582 -0.084780888 -0.204029057 0.0004766342 -0.0811054208
[9,] -0.171443865 -0.008836704 0.122122049 0.1343661270 0.2483131800
[10,] -0.107923868 0.062968092 -0.021221736 -0.0902549691 0.1758536741
[11,] -0.006150447 -0.077763967 0.088960459 0.3194424294 -0.0374330315
[12,] 0.057241515 0.001644633 -0.212314482 -0.0004988069 -0.1538886815
[13,] 0.137492659 0.005461060 -0.039217118 -0.1643495143 -0.1917291975
[14,] 0.254392257 -0.015294443 0.222652384 -0.0385711297 -0.0740680726
[15,] 0.251447078 -0.276454650 -0.281393910 0.0507517397 -0.0636237770
[16,] -0.131184126 -0.068934246 0.181066967 0.1610151215 -0.0763627731
[17,] 0.006838398 0.057362481 -0.031482716 0.0106740590 0.0532851484
[18,] -0.176523927 -0.074680481 0.176252473 0.0733182109 -0.0734166203
[19,] 0.185898477 0.149603750 -0.040057959 -0.0686546024 -0.0402677423
[20,] -0.054763689 0.132500961 0.038728807 -0.1850116253 0.0070467441
[21,] -0.118826692 -0.107506410 -0.178603712 -0.0639316781 -0.1082956759
[22,] 0.004358475 0.102163192 -0.107303487 -0.0254114813 -0.0743051454
[23,] -0.087268069 0.204818072 0.229324770 -0.0110115182 -0.0177331440
[24,] -0.038321042 0.091700958 0.073639216 -0.1170127251 -0.2410302545
[25,] 0.071497366 0.188230636 -0.316413574 0.2465106069 0.0966426866
[26,] 0.010195437 -0.121895937 0.054936399 0.1131771502 -0.0093023925
[27,] -0.032078555 -0.215539326 -0.033031376 -0.1007315762 0.1379805232
[28,] -0.015984490 -0.210270723 -0.031448224 -0.0159127067 -0.2183321163
[29,] 0.232372511 0.096226493 0.069384749 0.0067442165 -0.0003823659
[30,] -0.113747429 -0.311344029 -0.079429813 0.1848876219 0.0988188228
[31,] -0.077478600 -0.101529585 0.029755717 -0.1991813403 -0.0312260446
[32,] 0.303643070 -0.189781963 -0.130485814 -0.0660644832 0.1589775528
[33,] 0.221911290 0.157769106 -0.196016647 0.1945129613 0.3463047389
[34,] 0.161529561 -0.061965366 0.215395641 0.0478578061 -0.2577446726
[35,] -0.143463116 -0.013326934 -0.183369038 0.0582290295 -0.0037354399
[36,] -0.099456274 0.187299108 0.108145607 -0.0050035153 -0.0739485171
[37,] -0.010634051 0.071119054 0.049171577 0.1317909266 -0.1769870597
[38,] 0.167388545 -0.088904850 0.075832498 0.0419957778 -0.0810714569
[39,] 0.277264231 -0.175251411 0.189659991 -0.1204234444 0.3400268424
[40,] -0.085207424 -0.040470257 0.183611802 -0.0155673234 0.0378818166
[41,] -0.275619860 -0.131912796 -0.183605562 -0.1182747041 0.2045886505
[42,] -0.119918869 0.050818687 0.141197264 0.1431877507 0.1413019778
[43,] -0.088291123 0.158954898 -0.109634415 -0.3040542866 -0.1339340765
[44,] -0.128266316 0.323589567 0.004260433 -0.1767044100 0.1165840650
[45,] -0.117778564 -0.072696204 0.012225975 0.1604106745 -0.0629770555
[46,] -0.113507122 0.058552059 0.014734622 -0.0563664438 0.0735585651
[47,] 0.133329897 0.003185259 0.119718834 0.2497129385 -0.2112170930
[48,] 0.234940487 0.246539542 0.031528428 -0.0559989375 0.0704199578
[49,] -0.118068676 -0.102618722 0.013900611 -0.0667181191 -0.1252918941
[50,] -0.024748802 -0.072694420 0.229436483 0.0782495958 0.1363255266
PC26 PC27 PC28 PC29 PC30
[1,] 0.054050182 0.2409224331 -0.0004764633 -0.312047287 -0.179192921
[2,] 0.165324087 0.1417371609 -0.0717683420 0.118589515 -0.067540476
[3,] -0.194085038 0.0617887178 0.0597487348 -0.192244373 0.032385734
[4,] 0.123397425 0.2379047173 0.1178953664 0.048190852 0.098201056
[5,] -0.153414774 -0.0158804658 -0.1987305118 0.180488110 0.067631908
[6,] -0.152191571 -0.0300744838 -0.1852879662 -0.075660371 -0.035336100
[7,] -0.051956503 0.2154881164 -0.0221571590 0.277607848 0.075440554
[8,] -0.024622020 -0.0503638810 0.2896571303 -0.303455434 -0.036210407
[9,] 0.188610581 -0.1997975344 -0.0554931035 -0.022447866 0.122863577
[10,] 0.093149661 0.1525521931 0.0349944299 -0.120688559 -0.034831399
[11,] -0.146632422 0.0004717992 0.0765210340 0.025024306 0.010469475
[12,] 0.257604723 0.0824108648 -0.1510385600 -0.090098338 0.239075718
[13,] 0.101184282 -0.1631476432 0.1457509351 0.141728945 -0.238143570
[14,] 0.138195154 0.0263092899 -0.0854283323 -0.009986356 0.051108863
[15,] -0.102976579 0.0712261879 0.0065800426 0.078339616 0.006337413
[16,] 0.236326483 0.1913527674 -0.0760196185 -0.054299277 -0.050990383
[17,] -0.396797577 0.0836422465 -0.0450094760 0.256412201 -0.189284157
[18,] -0.149127956 -0.0087746953 0.0638139201 -0.005032653 -0.290560184
[19,] -0.033379497 -0.0970056972 -0.1056733205 -0.142668312 0.163478465
[20,] -0.017318915 -0.0068731308 0.2832758765 0.275834411 0.096697467
[21,] 0.055268456 -0.1828257625 -0.1053083552 0.127599822 -0.166366815
[22,] 0.068223993 0.1071881434 0.1737075401 0.129113161 -0.076272372
[23,] 0.014437144 -0.2912030693 -0.0585991667 0.158437445 0.078092865
[24,] 0.109672742 0.1270318055 0.1538959793 0.064505663 -0.172089325
[25,] 0.022368181 0.1171047634 -0.1638685712 0.064775237 0.027555030
[26,] -0.317607670 -0.1358552047 -0.0308303621 -0.003824004 0.267381226
[27,] -0.096059983 -0.1726017813 0.0025284254 -0.022485024 0.023944277
[28,] 0.026225033 -0.0417264373 -0.2642453329 0.045293280 0.250850086
[29,] 0.127137553 0.0254240889 0.0116270536 -0.142740873 0.007017237
[30,] 0.043812609 -0.0545106726 -0.0715086291 -0.021294548 -0.360392229
[31,] 0.017934114 -0.2227909663 0.0118018448 0.013905284 -0.171226224
[32,] -0.089896565 -0.0924654598 -0.0111639605 -0.114461944 -0.009429399
[33,] 0.218594297 -0.0923528688 0.3109835777 0.197035898 0.008203404
[34,] -0.058625326 -0.0281240556 0.2548710415 -0.079161729 0.039480253
[35,] -0.190424510 0.1230845868 0.1474413764 0.015709550 -0.032004164
[36,] 0.045006177 0.2292673561 -0.0544331556 -0.132837183 -0.138109418
[37,] 0.092539552 -0.0712268880 -0.3770233640 0.053673126 -0.156316826
[38,] 0.251181022 -0.1160308432 0.0335499317 -0.006160551 0.044587881
[39,] 0.010006710 0.0731408434 -0.2239191352 -0.051761023 -0.181736997
[40,] -0.168076280 0.2410095302 -0.0716786553 -0.205289866 0.094298935
[41,] 0.211959330 -0.1138999813 -0.0158028227 -0.021939039 0.190322140
[42,] -0.063954178 -0.1758219322 0.1140918443 -0.184978128 0.098249780
[43,] 0.005503398 -0.0935825454 0.0523777482 0.011146979 0.125546484
[44,] -0.075015332 -0.3028894638 -0.1442206706 -0.184531884 -0.134533557
[45,] -0.118181656 0.0471605309 0.1511954245 0.038470688 0.170573812
[46,] -0.134980637 0.0094067902 0.0259998346 -0.149135998 0.173941818
[47,] 0.093632520 -0.1216994601 0.1792566588 -0.150817975 0.008097333
[48,] -0.115032234 0.1034274331 -0.0233955631 -0.009831447 -0.005706415
[49,] 0.041754319 0.2283319648 -0.0653484626 0.153145837 0.233022252
[50,] -0.001771063 -0.0332582634 -0.0238324522 0.271681826 -0.009426303
PC31 PC32 PC33 PC34 PC35
[1,] 0.01095345 0.154714455 0.044800026 -0.138107138 -0.154726252
[2,] 0.14671488 -0.097697227 -0.057921837 -0.251629625 0.089258591
[3,] 0.11207795 0.016080920 0.026202362 0.231871876 0.212737552
[4,] -0.14097075 0.023688932 0.082523958 -0.236282027 0.245272762
[5,] -0.32410177 0.213292405 -0.008021793 -0.031995333 -0.059216445
[6,] -0.12402717 -0.168034051 0.099929801 0.043666978 0.153756927
[7,] -0.18828746 -0.130497881 0.024308653 -0.023850032 0.114063235
[8,] -0.10185744 -0.017142232 -0.286021050 -0.157230038 -0.074253787
[9,] 0.13815394 0.037742040 0.021861646 0.184442048 -0.083036688
[10,] -0.07943763 -0.045240444 -0.149590020 0.127408777 -0.272515137
[11,] 0.01961550 -0.015847529 -0.098000339 0.088576119 -0.157855014
[12,] 0.01705258 0.010013171 0.034761806 -0.184389082 -0.016802382
[13,] -0.14386590 -0.327788888 -0.121864773 -0.056757803 0.220742169
[14,] 0.13069454 -0.217716795 -0.077399846 0.229952369 -0.187149002
[15,] 0.25929027 0.042133570 0.332441989 -0.030111633 0.119132198
[16,] 0.04344216 -0.082405305 0.029641181 0.069606860 -0.021194886
[17,] 0.19633815 -0.075761051 0.094803467 0.087388080 -0.054600369
[18,] 0.01017904 0.155331086 0.015689527 -0.015098677 -0.032590475
[19,] 0.18001991 0.240060357 -0.066215683 0.020928919 -0.183325303
[20,] 0.12061385 0.131437332 0.229740109 -0.105340324 0.047884757
[21,] -0.06208806 0.057023176 0.251447288 -0.191447320 -0.221496136
[22,] 0.18412048 0.142450551 -0.043176172 0.287612674 -0.054050287
[23,] 0.14502476 -0.007505363 -0.274834083 -0.007805624 0.228460420
[24,] -0.17526643 0.061604888 0.003863575 0.231994015 -0.048178969
[25,] -0.03718864 -0.114253253 -0.125749585 -0.109713751 -0.112059724
[26,] -0.03085785 0.026000631 -0.126572757 -0.237352841 -0.218128062
[27,] -0.05590564 -0.076256156 -0.000515412 0.216156546 0.135678426
[28,] -0.15681744 0.273882115 -0.138725181 0.027411659 0.164601476
[29,] -0.07204092 -0.008893880 0.047050003 0.039252051 0.223161443
[30,] -0.09416527 0.135505266 0.100604660 0.038895309 -0.008605694
[31,] 0.17836072 -0.218327506 -0.125031676 -0.117246283 -0.166554937
[32,] 0.04598101 -0.101853185 -0.188285560 0.021119386 0.276950775
[33,] 0.08687215 0.133839736 0.027513141 -0.052600329 -0.021580381
[34,] 0.15072337 0.092255026 -0.003592337 -0.239639626 0.041779902
[35,] -0.09816963 0.183483291 -0.299061206 0.260249882 0.061107734
[36,] 0.19272206 0.104276425 -0.186462434 -0.187637952 0.210464921
[37,] 0.17369333 -0.042323460 -0.010907551 0.085016074 0.088233094
[38,] 0.07601618 0.233451846 0.032050429 0.061354604 -0.116907001
[39,] -0.09715404 -0.150452898 -0.003934985 -0.084256338 -0.128024825
[40,] 0.11190781 -0.111957824 0.162901617 -0.009075269 0.032953012
[41,] -0.07507798 -0.048102927 -0.050607974 0.136155316 0.094673151
[42,] -0.04759536 -0.033308076 0.298158114 0.102116925 0.047989936
[43,] 0.01097223 -0.324827300 0.110746292 0.058928518 -0.244888290
[44,] -0.11575237 0.204207988 0.205909400 -0.107886031 0.105537675
[45,] -0.15694018 -0.214980233 -0.029420446 -0.153705180 -0.071785497
[46,] 0.25685793 -0.104911280 0.033113576 -0.047879670 -0.003659788
[47,] -0.31782575 -0.107970954 0.213543996 0.043648679 -0.001912376
[48,] -0.20996276 0.103703972 -0.057076365 0.049623850 -0.139150082
[49,] -0.03360435 -0.011412800 0.162661601 0.166548232 -0.032230640
[50,] -0.01850972 0.106669430 -0.176561977 -0.129187770 -0.093470491
PC36 PC37 PC38 PC39 PC40
[1,] -0.197942719 0.2200722917 0.064685169 -0.0764512988 -0.121881079
[2,] 0.227786008 0.1046237452 -0.136984377 0.0157833032 -0.111374142
[3,] 0.079741166 -0.0466337679 -0.219617224 -0.1384384415 0.250763990
[4,] -0.080149946 0.0805421196 0.007106110 0.1543600694 -0.040958815
[5,] -0.118542353 -0.1664040292 -0.225812545 -0.0732924809 0.160049793
[6,] -0.092761217 0.2589845920 -0.084584169 0.1957743146 0.089088102
[7,] 0.075919180 -0.0192600332 0.019925416 -0.1315542885 0.077013522
[8,] 0.125421817 -0.0244069973 0.169982120 0.1253923591 0.033561940
[9,] 0.062002576 -0.0594187341 -0.158133375 -0.1373018679 0.209808607
[10,] -0.099694471 -0.1961393226 0.167255642 0.2029690171 0.131301090
[11,] -0.269170510 0.0006550095 -0.112036312 -0.0479775684 0.102799943
[12,] 0.046060673 -0.0573156939 -0.036278033 0.1215049701 0.133912563
[13,] -0.155862415 0.1263662421 -0.002471933 0.0115697801 0.287884378
[14,] -0.051909953 0.3585365815 0.001416975 -0.0907478805 -0.107741678
[15,] -0.128543600 -0.0470074602 -0.046663243 0.1768349936 0.205047590
[16,] -0.224313566 -0.1112339699 -0.082488910 -0.0084306299 0.222454046
[17,] -0.112594794 -0.1707938623 -0.067571955 0.2028440258 -0.269765053
[18,] 0.100591064 0.2058488443 0.242400871 -0.1750689756 0.102429995
[19,] -0.156604006 0.0580855909 -0.018219708 0.0683932741 -0.021103159
[20,] 0.066677629 0.0919877972 0.044487390 -0.1165961090 0.010480284
[21,] -0.106819466 0.0271003294 0.245881223 -0.2280878361 0.059506416
[22,] 0.280571400 0.0801388711 0.005394423 0.1454355611 0.146364652
[23,] 0.009895848 0.1133144514 0.192797508 0.1001935242 -0.078637506
[24,] 0.075255560 -0.0565815723 -0.193129110 0.2766497085 -0.223439109
[25,] 0.059813660 -0.1612678189 -0.068082058 -0.2075966023 -0.204087050
[26,] 0.205496425 0.0496604484 0.051968121 0.1184606995 0.205353229
[27,] 0.111585506 -0.2374545356 0.204222499 0.1208991528 -0.212502130
[28,] -0.016703021 0.0330429480 0.062808722 0.2425505591 -0.205100360
[29,] 0.065733460 -0.2136694170 0.085157278 -0.2297307817 0.098205891
[30,] 0.040147906 0.1941230904 -0.135049722 -0.0026121748 -0.188122279
[31,] 0.096745711 -0.1671138849 -0.239053458 0.0400020773 -0.012711865
[32,] -0.105028037 0.2637573817 0.022222363 -0.1042498174 -0.128942553
[33,] 0.040087104 -0.0693434705 0.145805994 0.1182010971 0.002841752
[34,] 0.001425711 -0.2591498636 -0.159322952 -0.2360188948 -0.220285937
[35,] -0.073297207 -0.0748434669 0.104641293 -0.2169739799 0.110163277
[36,] -0.153252881 -0.1552975175 -0.059190194 0.0279013679 -0.046861396
[37,] 0.218634701 -0.2092393492 0.191899106 -0.1594874547 0.004865832
[38,] 0.137870107 0.1414313038 -0.129131564 0.0175635155 -0.031141936
[39,] 0.142070251 -0.1382493943 0.094455827 0.0753340937 0.019317586
[40,] 0.328450174 0.1147273302 0.034044166 0.1739899410 0.149122985
[41,] -0.081251607 0.0231936896 -0.214399438 -0.1355108024 -0.107506862
[42,] -0.077491014 -0.0368897337 -0.168228812 0.0008449374 -0.148004296
[43,] -0.097269672 0.0332534267 0.012209599 0.0423375065 -0.062071560
[44,] 0.050367910 0.0116421109 -0.029838750 0.0389296439 0.079603571
[45,] 0.174434609 0.1026957494 -0.166954529 -0.1449683180 -0.064185169
[46,] -0.220066923 -0.0186452817 0.198817448 -0.0818393135 -0.128687747
[47,] -0.034062844 -0.1568618427 0.181520675 0.0977143406 -0.074734901
[48,] 0.211687364 0.1278250966 -0.140988221 -0.1791271152 -0.105986884
[49,] -0.040788779 0.0577191677 0.325281417 -0.1611719384 -0.108816350
[50,] -0.246689412 0.0492601299 -0.052542974 0.1244773183 0.120714894
PC41 PC42 PC43 PC44 PC45
[1,] -0.0958882279 -0.0738677769 0.240613491 0.160426265 0.061920876
[2,] -0.0769814218 -0.2179205401 -0.076463309 0.084155807 -0.051995352
[3,] 0.1907299231 0.0966256912 0.086165811 -0.222432578 -0.138035208
[4,] 0.2504986366 0.0794424270 -0.222489334 0.177010545 -0.150075652
[5,] 0.0129025843 -0.3154684528 0.139711256 0.043010662 0.025633475
[6,] 0.1774670482 -0.2018862001 0.123337736 0.147643038 0.091313217
[7,] -0.2102969511 0.1135321673 -0.087945483 -0.060382833 -0.282558616
[8,] -0.0087650818 -0.1120429533 0.085853549 0.192971247 -0.208447197
[9,] 0.0778324458 -0.1905674313 -0.225787586 0.108018388 -0.017384330
[10,] 0.1856344199 -0.0764849528 -0.071558923 -0.257830406 0.058709099
[11,] 0.2054370719 0.3050676130 0.024741086 -0.041733526 -0.065227293
[12,] -0.1339153847 0.2017164809 -0.230770043 0.281150516 0.020432080
[13,] -0.1557753682 0.0379008592 0.070641814 -0.096064443 0.061967846
[14,] 0.0310236284 -0.0980702024 -0.080471187 0.081493318 -0.139389319
[15,] -0.1863497043 -0.0114443096 -0.024432858 -0.118695564 -0.057380507
[16,] -0.1528208103 -0.2358439929 0.089150598 -0.024258756 -0.081395046
[17,] -0.0036726194 -0.0297150288 -0.077174507 0.280352076 0.073864764
[18,] -0.0344509622 0.0342177047 0.033432067 -0.020790547 0.076341095
[19,] -0.0431485314 -0.0978812125 -0.165560566 -0.002672882 -0.310244913
[20,] 0.2043355456 0.1489154739 0.153367672 0.144447491 -0.103038451
[21,] 0.2899217364 -0.0087614300 -0.163884394 -0.150558668 -0.075389632
[22,] 0.0304039930 -0.1770071441 0.130260871 0.088416392 0.234544083
[23,] -0.0421842436 0.0029053987 0.158713551 -0.043395692 -0.163417079
[24,] 0.0067912113 0.1367161847 -0.097154949 -0.151418759 0.086064969
[25,] 0.0978300194 0.1194220530 0.294330518 -0.096060975 -0.173388415
[26,] -0.0256177694 0.0827176789 0.187495713 0.017338421 0.119687238
[27,] 0.0322330827 -0.2619504332 0.057723987 -0.016975213 -0.286730636
[28,] 0.1702363183 0.1126436572 -0.024338455 -0.105693239 0.188900107
[29,] 0.3778663158 0.0308932072 0.056886135 0.284706837 0.295090662
[30,] 0.0993430455 0.0390374997 -0.034198140 -0.035190905 -0.083943770
[31,] -0.0116741764 0.1652327842 -0.126563270 0.164026493 0.153504480
[32,] 0.0574647217 -0.0547499301 -0.154891509 -0.040141194 0.106840632
[33,] -0.0291319212 -0.0696926378 -0.016232475 -0.221633404 0.131884786
[34,] 0.0086031963 -0.3008026406 0.027146827 -0.016738044 -0.004604820
[35,] -0.2463261121 0.1958635847 -0.218253820 0.279991539 -0.074453237
[36,] -0.0008160286 0.1288512622 0.088187964 -0.272662773 -0.042490910
[37,] -0.0306125001 0.1017371018 -0.080945784 -0.014599122 0.001999623
[38,] -0.1116606788 0.2371229875 0.208628640 -0.036896844 -0.073951580
[39,] -0.1269065965 0.1313875448 0.203696682 0.064721950 0.084671586
[40,] 0.0805093143 0.0204664616 -0.031757438 -0.125030015 -0.073508070
[41,] -0.0803563507 0.0398064644 0.189416223 -0.031751401 0.166109844
[42,] -0.2008224137 0.1605496741 0.180835601 0.099550196 -0.010040387
[43,] 0.1393766413 0.1121520350 0.059574544 -0.003457477 -0.113031629
[44,] -0.2392466813 0.0003311728 -0.106672882 -0.086601497 0.019642965
[45,] -0.0730628174 -0.1289193081 -0.135722643 -0.252620512 0.158112938
[46,] -0.1138019752 0.0514188653 -0.178028081 -0.152554430 0.366867682
[47,] -0.1120573066 0.0122260518 -0.114930323 0.024289302 -0.039761484
[48,] -0.0659081527 -0.0217788351 -0.262030705 -0.115436014 0.061081009
[49,] -0.2032469276 -0.0801853207 0.168519969 0.012801597 0.132207213
[50,] -0.0180292811 -0.0550343516 0.007065797 0.047183893 0.087159838
PC46 PC47 PC48 PC49 PC50
[1,] -0.168571259 -0.045439066 -6.409172e-02 -0.03931624 0.037422725
[2,] -0.012600496 -0.188961150 -5.760995e-02 -0.06995691 0.266172249
[3,] 0.036114184 0.006485126 -1.079845e-01 0.16464350 0.108179226
[4,] 0.031477794 -0.061876823 2.309806e-01 0.07701797 0.194119204
[5,] -0.026267090 -0.042450713 1.967080e-01 -0.08843569 0.042269743
[6,] 0.076171556 0.011495421 -2.068740e-02 0.05801410 0.154624520
[7,] 0.326726149 -0.002126200 -8.907648e-02 -0.13264885 -0.180301907
[8,] 0.210844444 0.061202935 -4.370732e-02 -0.06227198 -0.157201810
[9,] -0.084182575 -0.263286092 9.720912e-02 -0.18474916 -0.245041820
[10,] 0.125147604 0.177537465 2.015946e-01 -0.06446887 0.175583997
[11,] -0.285405029 -0.058138368 6.659986e-02 0.02081321 0.163621849
[12,] -0.178817511 0.094730678 1.273055e-01 0.16140030 -0.154919661
[13,] -0.046218279 -0.148882649 2.135598e-01 0.29131563 -0.053676827
[14,] -0.066455431 0.119759729 1.552191e-01 0.02590080 -0.211714322
[15,] -0.078108646 0.075687390 -1.289635e-01 -0.32017311 -0.100423993
[16,] 0.297211483 0.284808560 -1.676242e-01 0.17024767 -0.043924501
[17,] 0.137992241 -0.011484316 1.770664e-01 -0.03978012 -0.067037508
[18,] 0.151719964 -0.133147200 4.831709e-02 -0.23027921 -0.005538717
[19,] -0.024876955 -0.229060425 -1.745584e-01 0.05504448 0.160239927
[20,] -0.047950593 0.254218597 -1.618058e-01 0.04501852 0.133040341
[21,] 0.124174575 -0.277551591 -8.205588e-02 0.14907453 -0.142412888
[22,] -0.015859569 -0.102588926 -1.105360e-01 0.09666588 -0.022029115
[23,] -0.123032714 0.082079949 -1.388773e-01 -0.11866496 -0.178425460
[24,] -0.078276490 -0.191826182 1.221363e-02 -0.06517770 -0.137096248
[25,] 0.007775683 -0.101861308 -3.134927e-02 0.12054836 -0.117874540
[26,] 0.047952958 0.002187916 2.373825e-01 -0.06093553 -0.060940790
[27,] -0.221856474 -0.037180560 -5.566120e-02 0.26217295 0.091829130
[28,] 0.188197229 0.045322616 -1.322218e-01 0.07619079 -0.152784517
[29,] -0.055917923 0.027615252 -1.579064e-01 -0.09664651 -0.170974647
[30,] -0.117415890 0.386197913 5.956680e-02 0.06123558 -0.218812908
[31,] 0.105810624 -0.052329167 -2.066035e-01 0.09224888 0.072811632
[32,] 0.144454754 -0.084550735 9.332600e-02 -0.17698661 0.145143812
[33,] -0.017458748 0.043815198 1.671959e-01 0.05196241 -0.040479603
[34,] 0.038767329 0.137009360 2.140367e-01 0.03039667 -0.038625150
[35,] -0.116138910 0.067792715 2.219962e-02 0.04527967 0.029838017
[36,] -0.141467367 -0.172146466 5.230181e-02 -0.16848956 -0.153178872
[37,] 0.027471942 0.176469181 1.770070e-01 -0.07774936 0.346895581
[38,] 0.230420903 -0.017899631 1.497537e-01 0.06306640 0.293911186
[39,] -0.147597132 -0.057328570 -1.435141e-01 0.01215184 0.028898408
[40,] -0.034848558 -0.067761680 2.078880e-02 0.03089378 -0.098795957
[41,] 0.053040885 0.027557861 8.728948e-05 -0.29241629 0.084987658
[42,] 0.207251903 -0.216508374 5.326429e-02 0.17635218 -0.106634730
[43,] -0.029875499 0.203933306 3.824886e-02 -0.30490347 -0.013244735
[44,] -0.172840440 0.207577114 9.119002e-02 0.04520459 -0.009485349
[45,] -0.321831775 0.086600020 -1.364707e-01 0.02538020 0.066753843
[46,] 0.139334051 0.069800302 -8.728183e-02 0.21960891 -0.011357392
[47,] -0.030804975 -0.093701757 -2.183057e-01 -0.26817297 0.212514936
[48,] 0.129169001 0.092900505 -1.664521e-01 0.05263930 0.007782515
[49,] -0.151658482 -0.131595341 1.178141e-01 0.09556046 0.025103645
[50,] -0.063731943 0.052810299 -3.564141e-01 0.03589827 0.088449642
BatchQC documentation built on Nov. 8, 2020, 8:30 p.m.
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Description Usage Arguments Value Examples
Description
Performs principal component analysis and produces plot of the first two principal components
Usage
1 | batchqc_pca(data.matrix, batch, mod = NULL)
|
Arguments
data.matrix |
Given data or simulated data from rnaseq_sim() |
batch |
Batch covariate |
mod |
Model matrix for outcome of interest and other covariates besides batch |
Value
PCA object from principal component analysis
Examples
1 2 3 4 5 6 7 8 9 10 11 | nbatch <- 3
ncond <- 2
npercond <- 10
data.matrix <- rnaseq_sim(ngenes=50, nbatch=nbatch, ncond=ncond, npercond=
npercond, basemean=10000, ggstep=50, bbstep=2000, ccstep=800,
basedisp=100, bdispstep=-10, swvar=1000, seed=1234)
batch <- rep(1:nbatch, each=ncond*npercond)
condition <- rep(rep(1:ncond, each=npercond), nbatch)
pdata <- data.frame(batch, condition)
modmatrix = model.matrix(~as.factor(condition), data=pdata)
batchqc_pca(data.matrix, batch, mod=modmatrix)
|
Example output
sh: 1: cannot create /dev/null: Permission denied
Standard deviations (1, .., p=50):
[1] 5.37385516 1.24203430 1.20861596 1.14822039 1.07868428 1.04344750
[7] 0.98556583 0.97947654 0.92174077 0.91320945 0.89449780 0.86149785
[13] 0.84706775 0.82180281 0.78228239 0.76482753 0.74616903 0.72621231
[19] 0.68668468 0.67677100 0.65945857 0.63172156 0.62143893 0.57437768
[25] 0.55426563 0.54913491 0.51748897 0.50242423 0.49012697 0.47951732
[31] 0.46361561 0.42724253 0.41669333 0.38607166 0.36938047 0.34214576
[37] 0.31700973 0.29762569 0.28727510 0.28553312 0.25856150 0.24807391
[43] 0.21978999 0.17624031 0.16927586 0.15770845 0.14164507 0.11290626
[49] 0.10481578 0.07966933
Rotation (n x k) = (50 x 50):
PC1 PC2 PC3 PC4 PC5
[1,] 0.1428409 0.093906004 -0.09708496 0.098095278 -0.138884700
[2,] 0.1432312 -0.052758087 0.10416026 -0.014042349 0.049685604
[3,] 0.1365965 0.165763489 -0.16000022 0.098825776 -0.028820049
[4,] 0.1469878 -0.219091929 -0.04951724 -0.049684634 -0.047872749
[5,] 0.1432096 -0.047711504 -0.14473273 0.099669617 0.240824830
[6,] 0.1491981 0.070114109 0.01425394 0.079000459 -0.080750203
[7,] 0.1429338 0.132072602 -0.13705556 -0.050849739 -0.268729888
[8,] 0.1413007 0.069892777 -0.13885508 -0.108566261 0.264297425
[9,] 0.1463438 0.114626327 -0.26323460 0.008684241 -0.018485553
[10,] 0.1422389 -0.115896459 0.16688856 0.232385695 -0.143539494
[11,] 0.1372982 0.052880496 -0.07533488 -0.245358373 -0.207851109
[12,] 0.1379562 0.281255568 -0.04395646 0.144068813 -0.138330061
[13,] 0.1562253 0.119421687 0.07530289 -0.001775128 -0.016220709
[14,] 0.1361448 -0.135401686 0.20449879 0.158073402 0.187053235
[15,] 0.1454618 -0.248680002 0.16810132 0.036362378 0.017525777
[16,] 0.1494762 -0.107087833 -0.05799968 -0.155035063 0.027386310
[17,] 0.1451022 0.007961209 -0.18004497 0.005023514 0.051043323
[18,] 0.1282341 0.067293859 0.18149589 0.133104571 -0.229307603
[19,] 0.1418664 0.096316720 0.12728688 -0.014562895 -0.060107723
[20,] 0.1435351 0.189613624 0.02165129 0.152963057 0.168530308
[21,] 0.1556216 -0.099733483 -0.02627934 0.095822646 0.070996725
[22,] 0.1421520 -0.060135279 -0.17786720 -0.009941430 -0.166750425
[23,] 0.1368131 -0.168287016 -0.15896895 0.135336377 -0.141469857
[24,] 0.1454848 0.054482141 0.03939914 0.007426360 0.033462094
[25,] 0.1430666 -0.215989251 0.05196058 0.008788797 -0.112062597
[26,] 0.1407790 0.060908760 0.08991103 -0.184375825 0.074989542
[27,] 0.1514542 0.064435824 0.11010495 -0.128734611 -0.006757529
[28,] 0.1507267 -0.011617560 0.03129210 0.142512895 -0.127936950
[29,] 0.1471663 -0.212554490 0.14865359 -0.172602057 0.081994068
[30,] 0.1471254 0.146392440 -0.09911845 -0.132005666 0.034106696
[31,] 0.1355319 -0.157483834 0.12896004 -0.174241666 -0.130450890
[32,] 0.1434191 -0.010340115 -0.09677506 -0.094957364 0.014614964
[33,] 0.1458222 0.111118905 0.08458383 -0.016327089 0.085994647
[34,] 0.1417662 0.086506607 0.11232353 0.097662109 -0.387748104
[35,] 0.1447757 -0.252323247 0.12837721 0.188582955 0.071448301
[36,] 0.1397404 0.075581682 -0.02735131 -0.114777168 0.331256033
[37,] 0.1467416 0.214076244 0.04413713 0.092506613 0.209168072
[38,] 0.1288961 -0.303234776 -0.27240707 -0.065597009 0.089669429
[39,] 0.1333704 0.055220390 -0.16339313 0.246453943 -0.056409530
[40,] 0.1277452 -0.018300443 0.19110456 -0.049596150 0.026956740
[41,] 0.1261049 0.170624260 0.21726570 0.002551940 -0.079841560
[42,] 0.1335246 -0.002956071 0.24980722 0.241166323 0.199570562
[43,] 0.1449802 0.005032074 -0.04969729 -0.109199793 -0.016729685
[44,] 0.1333428 -0.269422953 0.01371882 -0.211486353 -0.156053862
[45,] 0.1323319 -0.213015485 -0.17435643 0.268533572 0.118758829
[46,] 0.1408328 0.035752536 -0.27653977 0.014759087 0.094089757
[47,] 0.1477849 0.070302812 -0.15680312 0.000778323 0.008954019
[48,] 0.1317724 0.143787614 0.13147013 -0.240469883 0.092266259
[49,] 0.1330103 -0.002890743 0.01845944 -0.389578225 -0.031174549
[50,] 0.1344629 0.154246751 0.21882797 -0.064156759 0.128102550
PC6 PC7 PC8 PC9 PC10
[1,] 1.057742e-01 -0.23538711 0.08386086 -0.042490448 0.106228703
[2,] 2.127898e-01 0.02892399 -0.07926812 -0.250263525 0.128446951
[3,] 2.915453e-01 0.23986862 0.01281772 0.241629294 -0.086788332
[4,] -8.877456e-03 0.06829730 0.19116250 0.266930310 -0.171680549
[5,] 7.478338e-02 -0.26904163 -0.13087882 -0.040797907 -0.004268275
[6,] 4.594550e-02 -0.00674125 0.16469339 0.099466542 0.023100654
[7,] -3.844750e-02 -0.17287273 -0.06680536 -0.019570467 0.202173661
[8,] -1.061109e-01 0.08911107 0.16578011 0.069245467 -0.055583334
[9,] 9.192449e-02 0.03184259 0.02780395 0.034390274 0.091813904
[10,] 8.516620e-02 -0.07790053 -0.28680431 -0.051243173 -0.126625608
[11,] -6.885604e-02 -0.10085691 0.14607128 -0.306814459 0.004118581
[12,] -1.347301e-02 0.10634248 -0.26411606 -0.031665758 -0.187959973
[13,] -2.065483e-01 -0.07175860 -0.06654491 0.030032905 0.061641044
[14,] 1.139226e-01 -0.01508137 0.09877166 0.239035719 0.085366149
[15,] 3.732541e-02 -0.05038467 0.10585356 0.101664049 -0.113483885
[16,] 2.064711e-02 0.19422998 0.10009077 -0.240337269 0.124151802
[17,] -2.489234e-01 0.15787775 -0.07613443 0.045882382 -0.013287985
[18,] -6.252651e-02 0.28965305 -0.26479355 0.134276256 0.067522482
[19,] -2.480382e-01 0.09791055 -0.11286878 0.032776989 0.198625081
[20,] 8.555796e-02 -0.04894219 -0.04787438 -0.104269659 0.189706624
[21,] -7.427736e-02 -0.03287849 0.23703666 -0.087858106 -0.161902588
[22,] -1.366387e-01 -0.08797062 -0.00150032 -0.009268987 -0.273208280
[23,] 1.156844e-01 -0.15023829 0.01017285 -0.088249286 -0.274122658
[24,] 1.887317e-01 0.09539473 0.16957954 0.027121172 0.301054245
[25,] 8.541816e-02 0.01305351 -0.14683465 0.254814297 0.039812151
[26,] 2.173556e-01 0.02062515 0.07578603 0.073635706 0.144239958
[27,] -9.440647e-02 -0.01892817 -0.09871189 -0.005641399 0.092442767
[28,] -9.183493e-05 0.06420247 0.09825811 -0.134786778 0.123207516
[29,] -1.487517e-01 0.04400108 -0.18710875 -0.053331849 0.173039351
[30,] 2.993303e-02 -0.16141993 -0.23577764 0.055983477 -0.036798606
[31,] 2.351830e-01 -0.21617188 -0.01983191 0.102927026 -0.029330750
[32,] 1.527496e-01 0.08609514 -0.16058057 -0.302782433 -0.026317495
[33,] 1.055833e-01 0.02958946 0.12841874 -0.085310656 0.126258415
[34,] -3.569113e-02 -0.01307430 0.16640043 -0.006521833 -0.082445301
[35,] 3.877703e-02 -0.07254960 0.15238727 -0.081458103 0.059246335
[36,] -6.812919e-02 0.03331068 -0.07354879 0.012493903 -0.139407213
[37,] -3.364137e-02 -0.06260033 0.18797769 0.031059751 -0.015924459
[38,] -2.283315e-01 -0.02056102 -0.13650870 0.059176147 0.045051991
[39,] -4.151309e-02 0.22920349 0.26342216 -0.110908262 -0.014999874
[40,] -2.519362e-01 -0.37118844 -0.00772624 -0.134642861 0.067441271
[41,] -3.579160e-01 -0.09643413 0.22688946 0.192797728 -0.035642121
[42,] 1.046422e-01 0.02813609 -0.12721625 -0.268383534 -0.238935158
[43,] -5.078433e-02 0.22231466 -0.02449162 -0.189289478 -0.061919470
[44,] 1.043704e-02 0.17861668 0.05556456 0.033439927 0.122353139
[45,] -2.339735e-01 0.19485836 -0.09112715 -0.022423759 0.045502871
[46,] 3.200647e-03 -0.21737615 -0.02807754 0.188034776 0.180365526
[47,] 1.392410e-01 -0.18910626 -0.11738840 0.186745558 -0.057392465
[48,] -3.346974e-02 -0.01360015 0.11936259 -0.075817863 -0.398787143
[49,] 1.789439e-01 0.14631769 -0.03384321 0.058552166 -0.168043756
[50,] -2.914245e-02 0.11187162 -0.13755855 0.209348365 -0.103254896
PC11 PC12 PC13 PC14 PC15
[1,] -0.001572544 -0.025974715 0.1028527090 0.3169193795 -0.220371867
[2,] 0.014643830 0.043274223 0.0722104070 -0.3829889251 -0.166768453
[3,] -0.199099361 -0.049204534 0.0822500485 -0.0386086957 -0.039800780
[4,] 0.021603322 -0.080032463 -0.1472446124 -0.0405373909 -0.036373310
[5,] -0.015850778 0.003971891 -0.0681253845 -0.1915098471 0.241337770
[6,] 0.222641735 -0.007899558 -0.1489148348 0.1749101128 0.236709533
[7,] 0.117247013 -0.089210452 0.0543867853 0.1833842482 -0.137319301
[8,] -0.071671804 0.313580721 0.1135565313 -0.0070633887 0.092834995
[9,] 0.160369038 0.303356345 -0.0028328523 0.1369204575 -0.048275771
[10,] -0.014256516 0.087717677 0.1308976338 0.1094219388 -0.068769016
[11,] 0.043986909 0.089164222 0.2367615932 -0.1986134162 0.041613226
[12,] -0.017374859 -0.129875698 0.0625206956 -0.0192922172 0.120335359
[13,] -0.008203427 0.162778489 0.0017158134 -0.0359413340 -0.120105043
[14,] 0.082426667 -0.089155072 0.3130974265 -0.1528451949 -0.005074339
[15,] 0.152831640 0.134518601 -0.0344526791 0.0255783119 -0.023442416
[16,] -0.110429020 -0.225027787 0.0182613560 -0.0286327553 0.090045988
[17,] -0.237917016 -0.032582814 0.2835440990 0.0391347922 -0.022352664
[18,] 0.167851224 -0.039418621 -0.0183441492 -0.1625123118 0.282661860
[19,] -0.219801350 -0.135327606 -0.2079683190 -0.0041655854 0.093654346
[20,] 0.056554416 0.098253275 0.1960658842 0.0275989511 0.131165578
[21,] -0.099094943 -0.186857501 0.0351263445 0.0627873355 -0.075657222
[22,] 0.081170897 -0.177309218 -0.0004306734 -0.1408558251 -0.255391879
[23,] -0.254809894 -0.087339937 -0.0871920914 -0.0056519045 0.091742482
[24,] -0.162326589 0.005461561 -0.2149585791 0.0641861884 -0.031553630
[25,] -0.086224482 0.191970488 -0.0314871801 -0.1342883312 -0.038332296
[26,] -0.008089449 -0.378796108 -0.0425453566 0.0365920766 -0.281025765
[27,] 0.384798803 -0.164401803 0.0446148983 0.0737688219 -0.038019601
[28,] 0.163514835 0.193272745 0.1982579990 -0.0007495177 -0.021009069
[29,] -0.078737959 -0.078188548 -0.0565589264 0.0108127341 -0.098782912
[30,] -0.079058730 -0.071328427 -0.2606803223 -0.0598080727 -0.002385048
[31,] 0.070285361 -0.067794005 0.0540622270 0.2566659061 0.350212381
[32,] -0.150899395 -0.001910786 -0.0157900396 0.1274311118 -0.007233154
[33,] -0.091260464 -0.094217689 -0.0174794962 0.0048745461 0.253423106
[34,] 0.020891902 0.106745421 -0.1405932804 0.0060755511 -0.053209651
[35,] 0.045444094 -0.042773903 -0.2009689758 -0.0043969283 0.009883379
[36,] 0.305287332 -0.204306826 0.1092495736 0.0848711852 0.086124225
[37,] -0.084847356 0.086948481 -0.0719572658 0.1764877744 -0.177140577
[38,] 0.146880744 0.074882842 -0.0518253681 0.1269040581 0.022266084
[39,] 0.050958264 0.041803354 -0.1189945153 -0.1854611727 0.143101651
[40,] -0.265727318 0.197137826 -0.0705886900 -0.0169971845 0.146584697
[41,] -0.153885089 -0.186102196 0.1241131592 -0.1019856951 0.067825301
[42,] 0.010242451 0.026182825 -0.0480929292 0.0235309705 -0.145524508
[43,] 0.182509144 0.038061946 -0.3599266531 -0.0797281607 -0.109261402
[44,] -0.061697972 0.115509597 0.2579300845 -0.0863525660 -0.122984110
[45,] -0.041593793 -0.083060492 0.0578308910 0.2988105123 0.030343540
[46,] 0.139060195 0.055819368 -0.1937205812 -0.3230992373 -0.023402058
[47,] -0.106882457 -0.100274480 0.1776645462 -0.1786404359 -0.031874712
[48,] 0.162874000 0.048320452 0.0499793759 -0.0746475432 0.032971397
[49,] -0.149286374 0.183544142 -0.0146956279 0.1779612297 0.209791844
[50,] -0.075741358 0.256123179 -0.1104181284 0.0895923465 -0.286742711
PC16 PC17 PC18 PC19 PC20
[1,] 0.157940786 0.029997504 -0.292465609 0.116430638 0.081323845
[2,] 0.044469208 -0.119015831 -0.014291059 -0.197078579 0.238355940
[3,] 0.078727526 -0.120676517 -0.062934337 0.032209482 0.269020548
[4,] 0.197469349 0.101007167 -0.067287300 0.065479732 -0.148918599
[5,] 0.101845576 -0.132819630 -0.036179960 0.150729456 -0.101538905
[6,] -0.158057265 -0.106833777 0.116158911 -0.123001138 0.086484819
[7,] 0.094961698 -0.293016113 0.202830099 -0.025857567 0.002680321
[8,] 0.100793592 -0.210478210 0.062321154 -0.060203688 -0.154150540
[9,] -0.033171701 0.251658296 -0.077850930 -0.069054593 0.031795454
[10,] -0.055140232 0.007899536 0.083566663 -0.315146759 -0.014189068
[11,] 0.111390406 -0.228296240 -0.042349380 -0.025970333 -0.141372850
[12,] -0.202428168 -0.162070486 -0.147334102 0.062569881 -0.080859865
[13,] 0.117031674 0.277425348 -0.071562592 -0.131925000 0.064835890
[14,] 0.007069339 -0.145547091 0.135915082 0.074453589 0.017458015
[15,] 0.067343136 -0.006582200 -0.136306461 -0.165260211 -0.156044495
[16,] -0.059205484 0.209746381 -0.165922334 0.093568636 -0.118393701
[17,] -0.019773630 0.086682418 -0.127331343 -0.048675822 0.187679957
[18,] 0.078554846 -0.039997840 -0.220578011 0.130852299 -0.109140063
[19,] 0.260366176 0.130715576 0.201397498 -0.183000843 -0.075862230
[20,] -0.176865095 0.270687263 0.106036033 -0.139057148 -0.217257230
[21,] -0.226515229 -0.105910708 0.036661107 -0.015672207 0.065481620
[22,] 0.069318633 0.039599648 0.277675750 0.198756099 -0.241158543
[23,] 0.012231926 -0.063444044 -0.248941922 -0.186833188 0.024968185
[24,] -0.208921914 -0.154284843 -0.146333519 -0.108900264 -0.263114318
[25,] -0.082311944 0.225114188 -0.083158233 0.181093859 -0.199646301
[26,] -0.055880242 0.168893707 -0.034321901 -0.138823126 -0.012896693
[27,] -0.131294543 -0.079744899 -0.231248829 0.054294631 -0.062946475
[28,] 0.228148421 0.190544412 0.058860041 0.126045389 0.155172403
[29,] 0.107142520 -0.171848675 -0.062820016 -0.193854758 0.091109649
[30,] 0.127327761 0.072790835 0.199499575 -0.149693049 0.059875261
[31,] 0.152347118 0.021626345 0.093468668 0.104308872 -0.007098285
[32,] -0.277771167 0.062275182 0.108793211 0.192989095 -0.267321777
[33,] 0.192620111 -0.108353344 -0.060098879 0.253154867 0.247383100
[34,] -0.166046633 -0.029359460 0.148716720 -0.015857986 0.096576370
[35,] -0.153823888 0.130421898 0.084841671 0.062132483 0.228641545
[36,] -0.089415136 0.087654310 0.240154945 0.023399155 0.085966066
[37,] 0.221031920 -0.051699124 -0.036402213 0.112272884 -0.202108616
[38,] -0.219521551 -0.127922824 -0.113295710 -0.084825550 0.215493295
[39,] -0.076179849 0.046022237 0.205187184 -0.142799897 0.029734045
[40,] -0.181758299 0.063396679 -0.026360018 0.257108153 0.139251692
[41,] -0.113743410 0.002060014 -0.007356113 -0.062399015 -0.028709703
[42,] 0.193953205 -0.097288505 0.074376446 0.009824625 -0.106708539
[43,] 0.092023612 0.050116970 -0.012218925 0.271901573 0.195800792
[44,] -0.083941040 -0.068066614 0.171978247 0.096643088 -0.066311941
[45,] 0.176325718 -0.028783676 0.002013910 0.011187741 -0.074683026
[46,] -0.026442812 -0.122666483 -0.067848564 -0.088397064 -0.101760956
[47,] -0.066724912 0.229008587 0.082032888 0.117671040 0.154318064
[48,] 0.006349858 0.156125287 -0.316058765 -0.186276444 0.025429292
[49,] 0.047460310 -0.014420762 0.192157806 -0.155014319 0.064137061
[50,] -0.210781328 -0.209457411 0.028513320 0.227555225 0.093777502
PC21 PC22 PC23 PC24 PC25
[1,] 0.023790050 0.045922678 -0.066189722 -0.1724427896 0.0738057514
[2,] -0.231859444 -0.041088949 -0.159015991 0.0190142393 -0.0404572285
[3,] 0.013426882 -0.092828422 -0.082675676 -0.1878235829 -0.0146970004
[4,] -0.093315341 -0.056007201 0.214795681 -0.0724890454 0.2294171887
[5,] 0.068253551 -0.014221205 0.028167604 -0.2565224685 -0.0782288162
[6,] -0.033162321 0.343095876 -0.170030662 0.3339797410 -0.0713892085
[7,] 0.056127239 0.092656234 0.039403397 -0.0316036192 0.1462774575
[8,] -0.094283582 -0.084780888 -0.204029057 0.0004766342 -0.0811054208
[9,] -0.171443865 -0.008836704 0.122122049 0.1343661270 0.2483131800
[10,] -0.107923868 0.062968092 -0.021221736 -0.0902549691 0.1758536741
[11,] -0.006150447 -0.077763967 0.088960459 0.3194424294 -0.0374330315
[12,] 0.057241515 0.001644633 -0.212314482 -0.0004988069 -0.1538886815
[13,] 0.137492659 0.005461060 -0.039217118 -0.1643495143 -0.1917291975
[14,] 0.254392257 -0.015294443 0.222652384 -0.0385711297 -0.0740680726
[15,] 0.251447078 -0.276454650 -0.281393910 0.0507517397 -0.0636237770
[16,] -0.131184126 -0.068934246 0.181066967 0.1610151215 -0.0763627731
[17,] 0.006838398 0.057362481 -0.031482716 0.0106740590 0.0532851484
[18,] -0.176523927 -0.074680481 0.176252473 0.0733182109 -0.0734166203
[19,] 0.185898477 0.149603750 -0.040057959 -0.0686546024 -0.0402677423
[20,] -0.054763689 0.132500961 0.038728807 -0.1850116253 0.0070467441
[21,] -0.118826692 -0.107506410 -0.178603712 -0.0639316781 -0.1082956759
[22,] 0.004358475 0.102163192 -0.107303487 -0.0254114813 -0.0743051454
[23,] -0.087268069 0.204818072 0.229324770 -0.0110115182 -0.0177331440
[24,] -0.038321042 0.091700958 0.073639216 -0.1170127251 -0.2410302545
[25,] 0.071497366 0.188230636 -0.316413574 0.2465106069 0.0966426866
[26,] 0.010195437 -0.121895937 0.054936399 0.1131771502 -0.0093023925
[27,] -0.032078555 -0.215539326 -0.033031376 -0.1007315762 0.1379805232
[28,] -0.015984490 -0.210270723 -0.031448224 -0.0159127067 -0.2183321163
[29,] 0.232372511 0.096226493 0.069384749 0.0067442165 -0.0003823659
[30,] -0.113747429 -0.311344029 -0.079429813 0.1848876219 0.0988188228
[31,] -0.077478600 -0.101529585 0.029755717 -0.1991813403 -0.0312260446
[32,] 0.303643070 -0.189781963 -0.130485814 -0.0660644832 0.1589775528
[33,] 0.221911290 0.157769106 -0.196016647 0.1945129613 0.3463047389
[34,] 0.161529561 -0.061965366 0.215395641 0.0478578061 -0.2577446726
[35,] -0.143463116 -0.013326934 -0.183369038 0.0582290295 -0.0037354399
[36,] -0.099456274 0.187299108 0.108145607 -0.0050035153 -0.0739485171
[37,] -0.010634051 0.071119054 0.049171577 0.1317909266 -0.1769870597
[38,] 0.167388545 -0.088904850 0.075832498 0.0419957778 -0.0810714569
[39,] 0.277264231 -0.175251411 0.189659991 -0.1204234444 0.3400268424
[40,] -0.085207424 -0.040470257 0.183611802 -0.0155673234 0.0378818166
[41,] -0.275619860 -0.131912796 -0.183605562 -0.1182747041 0.2045886505
[42,] -0.119918869 0.050818687 0.141197264 0.1431877507 0.1413019778
[43,] -0.088291123 0.158954898 -0.109634415 -0.3040542866 -0.1339340765
[44,] -0.128266316 0.323589567 0.004260433 -0.1767044100 0.1165840650
[45,] -0.117778564 -0.072696204 0.012225975 0.1604106745 -0.0629770555
[46,] -0.113507122 0.058552059 0.014734622 -0.0563664438 0.0735585651
[47,] 0.133329897 0.003185259 0.119718834 0.2497129385 -0.2112170930
[48,] 0.234940487 0.246539542 0.031528428 -0.0559989375 0.0704199578
[49,] -0.118068676 -0.102618722 0.013900611 -0.0667181191 -0.1252918941
[50,] -0.024748802 -0.072694420 0.229436483 0.0782495958 0.1363255266
PC26 PC27 PC28 PC29 PC30
[1,] 0.054050182 0.2409224331 -0.0004764633 -0.312047287 -0.179192921
[2,] 0.165324087 0.1417371609 -0.0717683420 0.118589515 -0.067540476
[3,] -0.194085038 0.0617887178 0.0597487348 -0.192244373 0.032385734
[4,] 0.123397425 0.2379047173 0.1178953664 0.048190852 0.098201056
[5,] -0.153414774 -0.0158804658 -0.1987305118 0.180488110 0.067631908
[6,] -0.152191571 -0.0300744838 -0.1852879662 -0.075660371 -0.035336100
[7,] -0.051956503 0.2154881164 -0.0221571590 0.277607848 0.075440554
[8,] -0.024622020 -0.0503638810 0.2896571303 -0.303455434 -0.036210407
[9,] 0.188610581 -0.1997975344 -0.0554931035 -0.022447866 0.122863577
[10,] 0.093149661 0.1525521931 0.0349944299 -0.120688559 -0.034831399
[11,] -0.146632422 0.0004717992 0.0765210340 0.025024306 0.010469475
[12,] 0.257604723 0.0824108648 -0.1510385600 -0.090098338 0.239075718
[13,] 0.101184282 -0.1631476432 0.1457509351 0.141728945 -0.238143570
[14,] 0.138195154 0.0263092899 -0.0854283323 -0.009986356 0.051108863
[15,] -0.102976579 0.0712261879 0.0065800426 0.078339616 0.006337413
[16,] 0.236326483 0.1913527674 -0.0760196185 -0.054299277 -0.050990383
[17,] -0.396797577 0.0836422465 -0.0450094760 0.256412201 -0.189284157
[18,] -0.149127956 -0.0087746953 0.0638139201 -0.005032653 -0.290560184
[19,] -0.033379497 -0.0970056972 -0.1056733205 -0.142668312 0.163478465
[20,] -0.017318915 -0.0068731308 0.2832758765 0.275834411 0.096697467
[21,] 0.055268456 -0.1828257625 -0.1053083552 0.127599822 -0.166366815
[22,] 0.068223993 0.1071881434 0.1737075401 0.129113161 -0.076272372
[23,] 0.014437144 -0.2912030693 -0.0585991667 0.158437445 0.078092865
[24,] 0.109672742 0.1270318055 0.1538959793 0.064505663 -0.172089325
[25,] 0.022368181 0.1171047634 -0.1638685712 0.064775237 0.027555030
[26,] -0.317607670 -0.1358552047 -0.0308303621 -0.003824004 0.267381226
[27,] -0.096059983 -0.1726017813 0.0025284254 -0.022485024 0.023944277
[28,] 0.026225033 -0.0417264373 -0.2642453329 0.045293280 0.250850086
[29,] 0.127137553 0.0254240889 0.0116270536 -0.142740873 0.007017237
[30,] 0.043812609 -0.0545106726 -0.0715086291 -0.021294548 -0.360392229
[31,] 0.017934114 -0.2227909663 0.0118018448 0.013905284 -0.171226224
[32,] -0.089896565 -0.0924654598 -0.0111639605 -0.114461944 -0.009429399
[33,] 0.218594297 -0.0923528688 0.3109835777 0.197035898 0.008203404
[34,] -0.058625326 -0.0281240556 0.2548710415 -0.079161729 0.039480253
[35,] -0.190424510 0.1230845868 0.1474413764 0.015709550 -0.032004164
[36,] 0.045006177 0.2292673561 -0.0544331556 -0.132837183 -0.138109418
[37,] 0.092539552 -0.0712268880 -0.3770233640 0.053673126 -0.156316826
[38,] 0.251181022 -0.1160308432 0.0335499317 -0.006160551 0.044587881
[39,] 0.010006710 0.0731408434 -0.2239191352 -0.051761023 -0.181736997
[40,] -0.168076280 0.2410095302 -0.0716786553 -0.205289866 0.094298935
[41,] 0.211959330 -0.1138999813 -0.0158028227 -0.021939039 0.190322140
[42,] -0.063954178 -0.1758219322 0.1140918443 -0.184978128 0.098249780
[43,] 0.005503398 -0.0935825454 0.0523777482 0.011146979 0.125546484
[44,] -0.075015332 -0.3028894638 -0.1442206706 -0.184531884 -0.134533557
[45,] -0.118181656 0.0471605309 0.1511954245 0.038470688 0.170573812
[46,] -0.134980637 0.0094067902 0.0259998346 -0.149135998 0.173941818
[47,] 0.093632520 -0.1216994601 0.1792566588 -0.150817975 0.008097333
[48,] -0.115032234 0.1034274331 -0.0233955631 -0.009831447 -0.005706415
[49,] 0.041754319 0.2283319648 -0.0653484626 0.153145837 0.233022252
[50,] -0.001771063 -0.0332582634 -0.0238324522 0.271681826 -0.009426303
PC31 PC32 PC33 PC34 PC35
[1,] 0.01095345 0.154714455 0.044800026 -0.138107138 -0.154726252
[2,] 0.14671488 -0.097697227 -0.057921837 -0.251629625 0.089258591
[3,] 0.11207795 0.016080920 0.026202362 0.231871876 0.212737552
[4,] -0.14097075 0.023688932 0.082523958 -0.236282027 0.245272762
[5,] -0.32410177 0.213292405 -0.008021793 -0.031995333 -0.059216445
[6,] -0.12402717 -0.168034051 0.099929801 0.043666978 0.153756927
[7,] -0.18828746 -0.130497881 0.024308653 -0.023850032 0.114063235
[8,] -0.10185744 -0.017142232 -0.286021050 -0.157230038 -0.074253787
[9,] 0.13815394 0.037742040 0.021861646 0.184442048 -0.083036688
[10,] -0.07943763 -0.045240444 -0.149590020 0.127408777 -0.272515137
[11,] 0.01961550 -0.015847529 -0.098000339 0.088576119 -0.157855014
[12,] 0.01705258 0.010013171 0.034761806 -0.184389082 -0.016802382
[13,] -0.14386590 -0.327788888 -0.121864773 -0.056757803 0.220742169
[14,] 0.13069454 -0.217716795 -0.077399846 0.229952369 -0.187149002
[15,] 0.25929027 0.042133570 0.332441989 -0.030111633 0.119132198
[16,] 0.04344216 -0.082405305 0.029641181 0.069606860 -0.021194886
[17,] 0.19633815 -0.075761051 0.094803467 0.087388080 -0.054600369
[18,] 0.01017904 0.155331086 0.015689527 -0.015098677 -0.032590475
[19,] 0.18001991 0.240060357 -0.066215683 0.020928919 -0.183325303
[20,] 0.12061385 0.131437332 0.229740109 -0.105340324 0.047884757
[21,] -0.06208806 0.057023176 0.251447288 -0.191447320 -0.221496136
[22,] 0.18412048 0.142450551 -0.043176172 0.287612674 -0.054050287
[23,] 0.14502476 -0.007505363 -0.274834083 -0.007805624 0.228460420
[24,] -0.17526643 0.061604888 0.003863575 0.231994015 -0.048178969
[25,] -0.03718864 -0.114253253 -0.125749585 -0.109713751 -0.112059724
[26,] -0.03085785 0.026000631 -0.126572757 -0.237352841 -0.218128062
[27,] -0.05590564 -0.076256156 -0.000515412 0.216156546 0.135678426
[28,] -0.15681744 0.273882115 -0.138725181 0.027411659 0.164601476
[29,] -0.07204092 -0.008893880 0.047050003 0.039252051 0.223161443
[30,] -0.09416527 0.135505266 0.100604660 0.038895309 -0.008605694
[31,] 0.17836072 -0.218327506 -0.125031676 -0.117246283 -0.166554937
[32,] 0.04598101 -0.101853185 -0.188285560 0.021119386 0.276950775
[33,] 0.08687215 0.133839736 0.027513141 -0.052600329 -0.021580381
[34,] 0.15072337 0.092255026 -0.003592337 -0.239639626 0.041779902
[35,] -0.09816963 0.183483291 -0.299061206 0.260249882 0.061107734
[36,] 0.19272206 0.104276425 -0.186462434 -0.187637952 0.210464921
[37,] 0.17369333 -0.042323460 -0.010907551 0.085016074 0.088233094
[38,] 0.07601618 0.233451846 0.032050429 0.061354604 -0.116907001
[39,] -0.09715404 -0.150452898 -0.003934985 -0.084256338 -0.128024825
[40,] 0.11190781 -0.111957824 0.162901617 -0.009075269 0.032953012
[41,] -0.07507798 -0.048102927 -0.050607974 0.136155316 0.094673151
[42,] -0.04759536 -0.033308076 0.298158114 0.102116925 0.047989936
[43,] 0.01097223 -0.324827300 0.110746292 0.058928518 -0.244888290
[44,] -0.11575237 0.204207988 0.205909400 -0.107886031 0.105537675
[45,] -0.15694018 -0.214980233 -0.029420446 -0.153705180 -0.071785497
[46,] 0.25685793 -0.104911280 0.033113576 -0.047879670 -0.003659788
[47,] -0.31782575 -0.107970954 0.213543996 0.043648679 -0.001912376
[48,] -0.20996276 0.103703972 -0.057076365 0.049623850 -0.139150082
[49,] -0.03360435 -0.011412800 0.162661601 0.166548232 -0.032230640
[50,] -0.01850972 0.106669430 -0.176561977 -0.129187770 -0.093470491
PC36 PC37 PC38 PC39 PC40
[1,] -0.197942719 0.2200722917 0.064685169 -0.0764512988 -0.121881079
[2,] 0.227786008 0.1046237452 -0.136984377 0.0157833032 -0.111374142
[3,] 0.079741166 -0.0466337679 -0.219617224 -0.1384384415 0.250763990
[4,] -0.080149946 0.0805421196 0.007106110 0.1543600694 -0.040958815
[5,] -0.118542353 -0.1664040292 -0.225812545 -0.0732924809 0.160049793
[6,] -0.092761217 0.2589845920 -0.084584169 0.1957743146 0.089088102
[7,] 0.075919180 -0.0192600332 0.019925416 -0.1315542885 0.077013522
[8,] 0.125421817 -0.0244069973 0.169982120 0.1253923591 0.033561940
[9,] 0.062002576 -0.0594187341 -0.158133375 -0.1373018679 0.209808607
[10,] -0.099694471 -0.1961393226 0.167255642 0.2029690171 0.131301090
[11,] -0.269170510 0.0006550095 -0.112036312 -0.0479775684 0.102799943
[12,] 0.046060673 -0.0573156939 -0.036278033 0.1215049701 0.133912563
[13,] -0.155862415 0.1263662421 -0.002471933 0.0115697801 0.287884378
[14,] -0.051909953 0.3585365815 0.001416975 -0.0907478805 -0.107741678
[15,] -0.128543600 -0.0470074602 -0.046663243 0.1768349936 0.205047590
[16,] -0.224313566 -0.1112339699 -0.082488910 -0.0084306299 0.222454046
[17,] -0.112594794 -0.1707938623 -0.067571955 0.2028440258 -0.269765053
[18,] 0.100591064 0.2058488443 0.242400871 -0.1750689756 0.102429995
[19,] -0.156604006 0.0580855909 -0.018219708 0.0683932741 -0.021103159
[20,] 0.066677629 0.0919877972 0.044487390 -0.1165961090 0.010480284
[21,] -0.106819466 0.0271003294 0.245881223 -0.2280878361 0.059506416
[22,] 0.280571400 0.0801388711 0.005394423 0.1454355611 0.146364652
[23,] 0.009895848 0.1133144514 0.192797508 0.1001935242 -0.078637506
[24,] 0.075255560 -0.0565815723 -0.193129110 0.2766497085 -0.223439109
[25,] 0.059813660 -0.1612678189 -0.068082058 -0.2075966023 -0.204087050
[26,] 0.205496425 0.0496604484 0.051968121 0.1184606995 0.205353229
[27,] 0.111585506 -0.2374545356 0.204222499 0.1208991528 -0.212502130
[28,] -0.016703021 0.0330429480 0.062808722 0.2425505591 -0.205100360
[29,] 0.065733460 -0.2136694170 0.085157278 -0.2297307817 0.098205891
[30,] 0.040147906 0.1941230904 -0.135049722 -0.0026121748 -0.188122279
[31,] 0.096745711 -0.1671138849 -0.239053458 0.0400020773 -0.012711865
[32,] -0.105028037 0.2637573817 0.022222363 -0.1042498174 -0.128942553
[33,] 0.040087104 -0.0693434705 0.145805994 0.1182010971 0.002841752
[34,] 0.001425711 -0.2591498636 -0.159322952 -0.2360188948 -0.220285937
[35,] -0.073297207 -0.0748434669 0.104641293 -0.2169739799 0.110163277
[36,] -0.153252881 -0.1552975175 -0.059190194 0.0279013679 -0.046861396
[37,] 0.218634701 -0.2092393492 0.191899106 -0.1594874547 0.004865832
[38,] 0.137870107 0.1414313038 -0.129131564 0.0175635155 -0.031141936
[39,] 0.142070251 -0.1382493943 0.094455827 0.0753340937 0.019317586
[40,] 0.328450174 0.1147273302 0.034044166 0.1739899410 0.149122985
[41,] -0.081251607 0.0231936896 -0.214399438 -0.1355108024 -0.107506862
[42,] -0.077491014 -0.0368897337 -0.168228812 0.0008449374 -0.148004296
[43,] -0.097269672 0.0332534267 0.012209599 0.0423375065 -0.062071560
[44,] 0.050367910 0.0116421109 -0.029838750 0.0389296439 0.079603571
[45,] 0.174434609 0.1026957494 -0.166954529 -0.1449683180 -0.064185169
[46,] -0.220066923 -0.0186452817 0.198817448 -0.0818393135 -0.128687747
[47,] -0.034062844 -0.1568618427 0.181520675 0.0977143406 -0.074734901
[48,] 0.211687364 0.1278250966 -0.140988221 -0.1791271152 -0.105986884
[49,] -0.040788779 0.0577191677 0.325281417 -0.1611719384 -0.108816350
[50,] -0.246689412 0.0492601299 -0.052542974 0.1244773183 0.120714894
PC41 PC42 PC43 PC44 PC45
[1,] -0.0958882279 -0.0738677769 0.240613491 0.160426265 0.061920876
[2,] -0.0769814218 -0.2179205401 -0.076463309 0.084155807 -0.051995352
[3,] 0.1907299231 0.0966256912 0.086165811 -0.222432578 -0.138035208
[4,] 0.2504986366 0.0794424270 -0.222489334 0.177010545 -0.150075652
[5,] 0.0129025843 -0.3154684528 0.139711256 0.043010662 0.025633475
[6,] 0.1774670482 -0.2018862001 0.123337736 0.147643038 0.091313217
[7,] -0.2102969511 0.1135321673 -0.087945483 -0.060382833 -0.282558616
[8,] -0.0087650818 -0.1120429533 0.085853549 0.192971247 -0.208447197
[9,] 0.0778324458 -0.1905674313 -0.225787586 0.108018388 -0.017384330
[10,] 0.1856344199 -0.0764849528 -0.071558923 -0.257830406 0.058709099
[11,] 0.2054370719 0.3050676130 0.024741086 -0.041733526 -0.065227293
[12,] -0.1339153847 0.2017164809 -0.230770043 0.281150516 0.020432080
[13,] -0.1557753682 0.0379008592 0.070641814 -0.096064443 0.061967846
[14,] 0.0310236284 -0.0980702024 -0.080471187 0.081493318 -0.139389319
[15,] -0.1863497043 -0.0114443096 -0.024432858 -0.118695564 -0.057380507
[16,] -0.1528208103 -0.2358439929 0.089150598 -0.024258756 -0.081395046
[17,] -0.0036726194 -0.0297150288 -0.077174507 0.280352076 0.073864764
[18,] -0.0344509622 0.0342177047 0.033432067 -0.020790547 0.076341095
[19,] -0.0431485314 -0.0978812125 -0.165560566 -0.002672882 -0.310244913
[20,] 0.2043355456 0.1489154739 0.153367672 0.144447491 -0.103038451
[21,] 0.2899217364 -0.0087614300 -0.163884394 -0.150558668 -0.075389632
[22,] 0.0304039930 -0.1770071441 0.130260871 0.088416392 0.234544083
[23,] -0.0421842436 0.0029053987 0.158713551 -0.043395692 -0.163417079
[24,] 0.0067912113 0.1367161847 -0.097154949 -0.151418759 0.086064969
[25,] 0.0978300194 0.1194220530 0.294330518 -0.096060975 -0.173388415
[26,] -0.0256177694 0.0827176789 0.187495713 0.017338421 0.119687238
[27,] 0.0322330827 -0.2619504332 0.057723987 -0.016975213 -0.286730636
[28,] 0.1702363183 0.1126436572 -0.024338455 -0.105693239 0.188900107
[29,] 0.3778663158 0.0308932072 0.056886135 0.284706837 0.295090662
[30,] 0.0993430455 0.0390374997 -0.034198140 -0.035190905 -0.083943770
[31,] -0.0116741764 0.1652327842 -0.126563270 0.164026493 0.153504480
[32,] 0.0574647217 -0.0547499301 -0.154891509 -0.040141194 0.106840632
[33,] -0.0291319212 -0.0696926378 -0.016232475 -0.221633404 0.131884786
[34,] 0.0086031963 -0.3008026406 0.027146827 -0.016738044 -0.004604820
[35,] -0.2463261121 0.1958635847 -0.218253820 0.279991539 -0.074453237
[36,] -0.0008160286 0.1288512622 0.088187964 -0.272662773 -0.042490910
[37,] -0.0306125001 0.1017371018 -0.080945784 -0.014599122 0.001999623
[38,] -0.1116606788 0.2371229875 0.208628640 -0.036896844 -0.073951580
[39,] -0.1269065965 0.1313875448 0.203696682 0.064721950 0.084671586
[40,] 0.0805093143 0.0204664616 -0.031757438 -0.125030015 -0.073508070
[41,] -0.0803563507 0.0398064644 0.189416223 -0.031751401 0.166109844
[42,] -0.2008224137 0.1605496741 0.180835601 0.099550196 -0.010040387
[43,] 0.1393766413 0.1121520350 0.059574544 -0.003457477 -0.113031629
[44,] -0.2392466813 0.0003311728 -0.106672882 -0.086601497 0.019642965
[45,] -0.0730628174 -0.1289193081 -0.135722643 -0.252620512 0.158112938
[46,] -0.1138019752 0.0514188653 -0.178028081 -0.152554430 0.366867682
[47,] -0.1120573066 0.0122260518 -0.114930323 0.024289302 -0.039761484
[48,] -0.0659081527 -0.0217788351 -0.262030705 -0.115436014 0.061081009
[49,] -0.2032469276 -0.0801853207 0.168519969 0.012801597 0.132207213
[50,] -0.0180292811 -0.0550343516 0.007065797 0.047183893 0.087159838
PC46 PC47 PC48 PC49 PC50
[1,] -0.168571259 -0.045439066 -6.409172e-02 -0.03931624 0.037422725
[2,] -0.012600496 -0.188961150 -5.760995e-02 -0.06995691 0.266172249
[3,] 0.036114184 0.006485126 -1.079845e-01 0.16464350 0.108179226
[4,] 0.031477794 -0.061876823 2.309806e-01 0.07701797 0.194119204
[5,] -0.026267090 -0.042450713 1.967080e-01 -0.08843569 0.042269743
[6,] 0.076171556 0.011495421 -2.068740e-02 0.05801410 0.154624520
[7,] 0.326726149 -0.002126200 -8.907648e-02 -0.13264885 -0.180301907
[8,] 0.210844444 0.061202935 -4.370732e-02 -0.06227198 -0.157201810
[9,] -0.084182575 -0.263286092 9.720912e-02 -0.18474916 -0.245041820
[10,] 0.125147604 0.177537465 2.015946e-01 -0.06446887 0.175583997
[11,] -0.285405029 -0.058138368 6.659986e-02 0.02081321 0.163621849
[12,] -0.178817511 0.094730678 1.273055e-01 0.16140030 -0.154919661
[13,] -0.046218279 -0.148882649 2.135598e-01 0.29131563 -0.053676827
[14,] -0.066455431 0.119759729 1.552191e-01 0.02590080 -0.211714322
[15,] -0.078108646 0.075687390 -1.289635e-01 -0.32017311 -0.100423993
[16,] 0.297211483 0.284808560 -1.676242e-01 0.17024767 -0.043924501
[17,] 0.137992241 -0.011484316 1.770664e-01 -0.03978012 -0.067037508
[18,] 0.151719964 -0.133147200 4.831709e-02 -0.23027921 -0.005538717
[19,] -0.024876955 -0.229060425 -1.745584e-01 0.05504448 0.160239927
[20,] -0.047950593 0.254218597 -1.618058e-01 0.04501852 0.133040341
[21,] 0.124174575 -0.277551591 -8.205588e-02 0.14907453 -0.142412888
[22,] -0.015859569 -0.102588926 -1.105360e-01 0.09666588 -0.022029115
[23,] -0.123032714 0.082079949 -1.388773e-01 -0.11866496 -0.178425460
[24,] -0.078276490 -0.191826182 1.221363e-02 -0.06517770 -0.137096248
[25,] 0.007775683 -0.101861308 -3.134927e-02 0.12054836 -0.117874540
[26,] 0.047952958 0.002187916 2.373825e-01 -0.06093553 -0.060940790
[27,] -0.221856474 -0.037180560 -5.566120e-02 0.26217295 0.091829130
[28,] 0.188197229 0.045322616 -1.322218e-01 0.07619079 -0.152784517
[29,] -0.055917923 0.027615252 -1.579064e-01 -0.09664651 -0.170974647
[30,] -0.117415890 0.386197913 5.956680e-02 0.06123558 -0.218812908
[31,] 0.105810624 -0.052329167 -2.066035e-01 0.09224888 0.072811632
[32,] 0.144454754 -0.084550735 9.332600e-02 -0.17698661 0.145143812
[33,] -0.017458748 0.043815198 1.671959e-01 0.05196241 -0.040479603
[34,] 0.038767329 0.137009360 2.140367e-01 0.03039667 -0.038625150
[35,] -0.116138910 0.067792715 2.219962e-02 0.04527967 0.029838017
[36,] -0.141467367 -0.172146466 5.230181e-02 -0.16848956 -0.153178872
[37,] 0.027471942 0.176469181 1.770070e-01 -0.07774936 0.346895581
[38,] 0.230420903 -0.017899631 1.497537e-01 0.06306640 0.293911186
[39,] -0.147597132 -0.057328570 -1.435141e-01 0.01215184 0.028898408
[40,] -0.034848558 -0.067761680 2.078880e-02 0.03089378 -0.098795957
[41,] 0.053040885 0.027557861 8.728948e-05 -0.29241629 0.084987658
[42,] 0.207251903 -0.216508374 5.326429e-02 0.17635218 -0.106634730
[43,] -0.029875499 0.203933306 3.824886e-02 -0.30490347 -0.013244735
[44,] -0.172840440 0.207577114 9.119002e-02 0.04520459 -0.009485349
[45,] -0.321831775 0.086600020 -1.364707e-01 0.02538020 0.066753843
[46,] 0.139334051 0.069800302 -8.728183e-02 0.21960891 -0.011357392
[47,] -0.030804975 -0.093701757 -2.183057e-01 -0.26817297 0.212514936
[48,] 0.129169001 0.092900505 -1.664521e-01 0.05263930 0.007782515
[49,] -0.151658482 -0.131595341 1.178141e-01 0.09556046 0.025103645
[50,] -0.063731943 0.052810299 -3.564141e-01 0.03589827 0.088449642
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