Description Usage Arguments Value Examples
Compute log2(counts per mil reads) and library size for each sample
1 |
qcounts |
quantile normalized counts |
lib.size |
default is colsums(qcounts) |
list containing log2(quantile counts per mil reads) and library sizes
1 2 3 4 5 6 7 8 | 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)
data.matrix <- as.matrix(data.matrix)
log2CPM(data.matrix)
|
sh: 1: cannot create /dev/null: Permission denied
$y
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 13.99545 13.91064 14.19065 14.02899 14.15043 13.99802 14.52134 14.15598
[2,] 14.09683 14.25733 13.89770 14.08199 14.34500 14.29178 14.14444 13.91328
[3,] 14.16756 13.91572 13.99159 14.09861 14.32078 14.25928 14.31306 14.18599
[4,] 14.36581 14.16346 14.15698 14.11774 14.05814 14.05906 14.33643 14.14122
[5,] 14.04629 13.99455 14.05667 14.32945 14.26925 14.28014 14.16298 14.24564
[6,] 14.09240 14.28794 14.49533 14.11802 14.29713 14.02792 13.99742 14.16178
[7,] 13.95807 14.11849 14.24175 13.89077 14.50083 14.00893 14.03520 14.20553
[8,] 14.28243 14.24270 14.21272 14.34079 13.79935 14.13792 14.02674 14.26683
[9,] 14.36533 13.89450 14.21643 13.96280 13.92861 14.19511 14.20659 14.06229
[10,] 14.39407 14.14470 14.30857 13.84061 14.16258 14.29082 14.21707 14.21553
[11,] 13.77292 14.16269 14.40418 14.23455 13.98080 14.22122 14.23611 14.18287
[12,] 14.34865 14.35864 14.13268 14.08808 14.31266 13.96400 14.05708 14.14583
[13,] 14.31727 14.09763 14.19091 14.43440 13.93173 14.15330 14.32751 14.31538
[14,] 14.28256 14.32152 14.22063 14.22537 14.34007 14.45809 14.22344 14.44956
[15,] 14.03457 14.21722 14.39089 14.29249 14.07335 14.24750 14.48962 14.08923
[16,] 14.12369 14.31256 14.26094 14.16585 14.02417 14.24837 14.03830 14.16756
[17,] 14.18364 14.24392 14.33716 14.27250 14.34101 14.12632 14.23933 14.14834
[18,] 14.34601 14.21997 14.40542 13.81478 14.26443 14.31990 14.30756 14.44083
[19,] 14.40414 14.28008 14.39992 14.42926 14.42407 14.25978 14.09220 14.13505
[20,] 14.38335 14.09369 14.47123 14.36286 14.29858 14.42322 14.23804 14.23807
[21,] 14.05322 14.27530 13.98950 14.23677 14.24310 14.08089 14.51849 14.30355
[22,] 14.53313 14.32766 14.30233 14.18871 14.13195 14.26520 14.24087 14.05459
[23,] 14.27325 14.19573 14.34010 14.37572 14.27909 14.18043 14.54606 14.15431
[24,] 14.17136 14.11795 14.37083 14.21613 14.13019 14.12333 14.03786 14.53606
[25,] 14.29543 14.35320 14.36324 14.31369 14.29664 14.36067 14.13453 14.22454
[26,] 14.17596 14.65484 14.13079 14.29249 14.38028 14.31361 14.29031 14.28708
[27,] 14.12551 14.37897 14.05867 14.08577 14.38553 14.11925 14.39479 14.48085
[28,] 14.28557 14.29493 14.38033 14.29475 14.24297 14.27391 14.40513 14.09169
[29,] 14.09540 14.25198 14.16983 14.43360 14.38154 14.32923 14.23650 14.46563
[30,] 14.37466 14.30506 14.31204 14.22458 14.30112 14.61290 14.26113 14.27998
[31,] 14.40437 14.37618 14.33210 14.26765 14.24573 14.31134 14.48161 14.53787
[32,] 14.13749 14.37024 14.02989 14.55471 14.22895 14.27575 14.19100 14.13814
[33,] 14.17109 14.30858 14.32276 14.28594 14.42640 14.35629 14.31757 14.14416
[34,] 14.35606 14.43271 14.35108 14.43951 14.29385 14.16284 14.42807 14.64782
[35,] 14.14923 14.27925 14.41591 14.14193 14.49282 14.46035 14.23650 14.30904
[36,] 14.47261 14.56329 14.41279 14.40611 14.38496 14.32558 14.37388 14.32785
[37,] 14.34457 14.22643 14.50351 14.28303 14.42684 14.29938 14.34158 14.22083
[38,] 14.39070 14.36079 14.34057 14.37501 14.25798 14.30358 14.49501 14.43821
[39,] 14.38545 14.32974 14.47112 14.26509 14.25411 14.43245 14.36119 14.46036
[40,] 14.21487 14.33101 14.19234 14.57758 14.32411 14.41614 14.28372 14.18938
[41,] 14.40425 14.44171 14.12658 14.38976 14.66173 14.32380 14.28919 14.46529
[42,] 14.42952 14.34409 14.36808 14.33653 14.45588 14.62283 14.30609 14.11468
[43,] 14.58105 14.27254 14.15618 14.48541 14.40398 14.37670 14.41494 14.24967
[44,] 14.48803 14.29138 14.20848 14.28063 14.22259 14.15595 14.32509 14.41027
[45,] 14.46334 14.52298 14.45919 14.19114 14.49630 14.38522 14.35278 14.31996
[46,] 14.38077 14.24429 14.48720 14.34830 14.48869 14.40490 14.32715 14.49483
[47,] 14.36035 14.18391 14.31145 14.54293 13.91716 14.35559 13.99605 14.61273
[48,] 14.44328 14.58472 14.47924 14.84494 14.29737 14.46249 14.56432 14.41155
[49,] 14.54395 14.47975 14.40810 14.61944 14.49440 14.68118 14.31988 14.33850
[50,] 14.44092 14.59609 14.24463 14.31468 14.50041 14.23172 14.33438 14.37454
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 14.04547 14.22709 14.15924 14.15639 14.25140 14.43483 14.22963 14.22765
[2,] 14.17109 13.90813 14.02659 14.37491 14.13686 13.93918 13.96763 14.24366
[3,] 14.16094 14.32235 14.35372 14.16675 14.17180 14.03824 14.12891 14.08901
[4,] 13.96352 14.18262 14.16378 14.34931 13.94595 14.04415 14.28466 13.86062
[5,] 14.05489 14.01455 14.43107 14.46732 14.19623 14.28515 14.12597 14.08664
[6,] 13.98907 14.05280 14.48620 14.02953 14.16066 14.00638 14.21226 14.12130
[7,] 14.26465 14.11482 14.21478 14.26848 14.09901 14.29825 13.88098 14.31649
[8,] 14.16266 14.35763 14.28973 14.38404 14.56890 14.11097 14.35468 14.07710
[9,] 13.98952 14.37871 14.37809 14.14737 14.24793 13.96590 14.20900 14.11966
[10,] 13.95500 14.11278 13.95358 14.24223 13.93191 14.19816 14.17243 14.18247
[11,] 14.20497 14.19942 14.16855 14.11021 14.29819 14.23057 14.25992 14.41938
[12,] 14.20715 14.12711 14.37625 14.07737 14.45895 14.26089 14.17885 14.48776
[13,] 14.38617 14.26619 13.86589 14.32747 14.02640 14.16265 13.97646 14.14135
[14,] 14.15444 14.14044 14.02452 14.34324 13.99200 14.21636 14.07306 14.17657
[15,] 14.14284 14.10022 14.18808 14.26479 14.27282 14.14075 14.23201 13.95274
[16,] 14.44395 14.15407 14.20260 14.18196 14.33252 14.33390 14.22820 14.42614
[17,] 14.34299 14.28128 14.15647 14.22654 14.29505 14.25244 14.13972 14.15074
[18,] 14.37664 14.14897 14.17317 14.36539 14.15314 14.21529 14.30039 14.18899
[19,] 14.15005 14.33886 14.26182 14.12773 14.05736 14.53794 14.22343 14.28102
[20,] 14.26157 14.15082 13.87820 14.28113 14.26313 14.17495 14.28763 14.11979
[21,] 14.29148 14.11264 14.19548 14.08102 14.33242 14.21422 14.41844 14.38809
[22,] 14.22282 14.36486 14.29686 13.78644 14.31783 14.19381 14.13896 14.16986
[23,] 14.16622 14.37968 14.32197 14.20411 14.22378 14.28367 14.24562 14.29524
[24,] 14.07959 14.36791 14.11896 14.43520 14.31926 14.21957 14.08272 14.44817
[25,] 14.37561 14.22696 14.31168 14.33928 14.20912 14.18362 14.30243 14.20954
[26,] 14.34834 14.16323 14.22518 14.21414 13.77408 14.35405 14.49959 14.11679
[27,] 14.27104 14.17915 14.23203 14.34177 14.40446 14.23081 14.38515 14.23359
[28,] 14.36497 14.05250 14.25298 14.32165 14.16972 14.10121 14.51803 14.51054
[29,] 14.44352 14.33699 14.32804 14.26836 14.19383 14.27810 14.17540 14.31685
[30,] 14.08602 14.08147 14.36142 14.43795 14.47555 14.59233 14.17676 14.25713
[31,] 14.14163 14.19049 14.37136 14.31844 14.22249 14.39269 14.20332 13.99758
[32,] 14.33480 14.25028 14.32231 14.13609 14.46523 14.57052 14.37550 14.47927
[33,] 14.45046 14.42407 14.37288 14.36817 14.40964 14.23163 14.28477 14.67209
[34,] 14.29931 14.36376 14.06088 14.02279 14.26118 14.30800 14.28213 14.45468
[35,] 14.56784 14.44571 14.24111 14.31419 14.07950 14.28934 14.45882 14.28699
[36,] 14.34112 14.26226 14.33977 14.11669 14.43395 14.40214 14.36393 13.99326
[37,] 14.40907 14.20147 14.45078 14.39964 14.59014 14.34210 14.23936 14.31219
[38,] 14.38798 14.69636 14.52654 14.21031 14.59860 14.30330 14.32634 14.31565
[39,] 14.21736 14.37241 14.33051 14.39801 14.24620 14.50198 14.26422 14.41070
[40,] 14.67026 14.59309 14.35086 14.50652 14.39289 14.60602 14.20198 14.28285
[41,] 14.46874 14.37568 14.09293 14.43995 14.31087 14.61679 14.49335 14.41938
[42,] 14.42986 14.21671 14.27944 14.41967 14.49508 14.30386 14.57604 14.40096
[43,] 14.36313 14.49363 14.53055 14.11722 14.42691 13.98726 14.42501 14.52938
[44,] 14.49720 14.52991 14.55126 14.18461 14.18998 14.44908 14.55424 14.30476
[45,] 14.51594 14.41525 14.43659 14.40807 14.57546 14.30778 14.42989 14.44675
[46,] 14.25055 14.43470 14.51673 14.41678 14.38807 14.38223 14.46703 14.12959
[47,] 14.50639 14.14443 14.44427 14.33793 14.25716 14.41578 14.37625 14.51626
[48,] 14.29064 14.50929 14.52625 14.37943 14.47050 14.49836 14.58425 14.26048
[49,] 14.27434 14.51645 14.53697 14.52424 14.43069 14.35221 14.38494 14.57203
[50,] 14.43074 14.61482 14.24207 14.64773 14.33001 14.15869 14.27822 14.47072
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 14.25798 14.11244 13.99719 14.22507 13.83471 14.09099 13.96786 14.10340
[2,] 14.19660 14.30696 14.19419 14.37165 14.25564 14.29133 14.28842 14.02996
[3,] 14.20375 14.27604 14.19864 14.02922 14.06127 14.14500 14.02196 14.10186
[4,] 14.09144 14.23708 13.83323 14.12461 14.38284 14.06613 14.17695 14.32810
[5,] 14.30864 14.36723 14.08859 14.26644 13.90294 14.37590 14.14461 13.99345
[6,] 13.93920 14.04603 14.03494 13.98531 14.10475 14.18739 14.40585 14.35812
[7,] 14.03321 13.85123 14.00581 14.11478 13.98693 14.18435 14.16890 14.21008
[8,] 14.04617 14.17655 14.29075 14.23035 14.19424 14.13290 14.15081 14.17690
[9,] 14.34882 14.47323 14.09429 13.94849 14.17680 13.86150 14.13697 14.17948
[10,] 14.26602 14.05126 14.33480 13.91981 14.21698 14.45579 14.15104 14.04448
[11,] 14.10863 14.27838 14.21298 14.38376 13.91439 14.26029 14.25905 13.98691
[12,] 14.37747 14.07888 14.26403 14.20996 13.92763 14.27424 14.49618 13.91498
[13,] 14.24416 13.94054 14.23501 14.39631 14.29423 14.17541 14.11595 14.16354
[14,] 14.02877 14.22423 14.14824 14.20131 14.19848 14.46625 14.21831 14.45913
[15,] 14.13829 13.93653 14.07321 14.16842 14.54936 14.44085 14.30268 14.31526
[16,] 14.30647 14.50095 14.12612 14.17316 14.41121 14.29752 14.02361 14.02434
[17,] 14.38226 14.29692 14.47273 14.23406 14.14811 13.91632 14.12905 14.08251
[18,] 14.32921 14.17024 14.30318 14.14433 14.25917 14.45531 14.29255 13.83670
[19,] 14.30784 14.00124 14.35351 14.19813 14.46262 14.24531 14.00578 14.39598
[20,] 14.20449 14.32343 14.37002 14.15207 14.37330 14.12657 14.39298 14.07551
[21,] 14.04562 14.24395 14.28589 14.11647 14.26642 13.94360 14.56944 14.22640
[22,] 14.31173 14.37910 14.46824 14.52779 14.32468 14.44203 14.53766 14.03953
[23,] 14.33753 14.59185 14.30753 14.37837 14.15433 14.17730 14.29287 14.09806
[24,] 14.13158 14.31328 14.19790 14.31153 14.53026 14.23821 14.27199 14.40023
[25,] 14.57012 14.42952 14.20073 14.33166 14.57053 14.28347 14.43087 14.35345
[26,] 14.23516 14.21518 14.29179 14.13169 14.43175 14.30993 14.25536 14.47406
[27,] 14.26425 13.88152 14.44058 14.10423 14.18166 14.44262 14.21541 14.24779
[28,] 14.34926 14.15983 14.23116 14.06015 14.10320 14.29046 14.29224 13.96451
[29,] 14.36674 14.23913 14.11559 14.30688 14.46910 14.49574 13.97816 14.58350
[30,] 14.33067 14.41871 14.32930 14.33166 14.24629 14.31358 14.32012 14.48165
[31,] 14.17177 14.35159 14.25197 14.12899 14.13908 14.28838 14.01004 14.14558
[32,] 14.45179 14.51735 14.47731 14.14369 14.35990 14.47796 14.11643 14.26209
[33,] 14.44961 14.28295 14.37777 14.37696 14.15272 14.14308 14.05639 14.48612
[34,] 14.11623 14.34331 14.24733 14.42852 14.40272 14.28817 14.51824 14.42083
[35,] 14.34201 14.42381 14.47598 14.17316 14.46947 14.38205 14.39653 14.50992
[36,] 14.28348 14.34286 14.44869 14.34644 14.13757 14.50197 14.31741 14.36011
[37,] 14.22295 14.27674 14.25150 14.45767 14.22674 14.08421 14.31450 14.35683
[38,] 14.41824 14.47272 14.24184 14.31085 14.34899 14.35324 14.34257 14.49735
[39,] 14.33832 14.07712 14.28415 14.18397 14.50434 14.29698 14.60770 14.34395
[40,] 14.29126 14.41465 14.40717 14.51712 14.18143 14.27005 14.35650 14.51019
[41,] 14.18055 13.97440 14.48369 14.57629 14.32274 14.12107 14.68414 14.47397
[42,] 14.19956 14.31133 14.49095 14.44162 14.23535 14.54278 14.21462 14.36477
[43,] 14.60381 14.06071 14.34463 14.49216 14.48665 14.27556 14.16856 14.29973
[44,] 14.31800 14.57236 14.25707 14.33178 14.56102 14.34571 14.54309 14.36585
[45,] 14.40449 14.38041 14.54758 14.02052 14.41860 14.42526 14.26693 14.27783
[46,] 14.41919 14.55513 14.45540 14.67388 14.37734 14.45102 14.43921 14.63041
[47,] 14.25323 14.68650 14.50327 14.46288 14.17691 14.33982 14.55364 14.50095
[48,] 14.50659 14.34219 14.41547 14.72392 14.43497 14.30347 14.37421 14.22444
[49,] 14.38769 14.52261 14.40333 14.42360 14.59902 14.29730 14.23954 14.28819
[50,] 14.59942 14.32366 14.11742 14.52095 14.34083 14.41560 14.32891 14.73359
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 14.44767 14.44921 14.06162 13.70225 14.17826 13.79514 14.29249 14.15916
[2,] 14.51522 14.19766 14.05343 14.42936 14.00847 14.18888 14.34897 14.17624
[3,] 14.26962 14.13298 14.22691 13.93876 14.20057 14.19673 14.17983 14.40624
[4,] 14.01497 14.25742 14.14617 13.80539 13.79443 13.79883 14.14490 14.36803
[5,] 13.85871 14.12560 14.08971 14.13156 14.34070 14.09838 14.24102 14.01232
[6,] 14.01458 13.97545 14.30610 14.03490 14.14825 14.44819 13.90362 14.18830
[7,] 14.47092 14.15732 14.15861 14.17904 14.04662 14.37049 14.24456 13.98604
[8,] 14.05407 14.23461 14.24557 14.27748 14.02100 13.77685 14.07856 14.18819
[9,] 14.50017 14.34405 14.35492 14.12479 14.29749 14.37436 14.07362 14.12338
[10,] 14.50607 14.13898 14.05081 13.99329 14.30306 14.33007 14.35106 13.92094
[11,] 14.46875 14.00284 14.28302 14.40294 13.93440 14.20665 14.16576 14.17948
[12,] 14.33706 13.86038 14.38116 14.18186 14.32879 14.28785 14.19830 14.01269
[13,] 14.15231 14.24805 13.98989 14.36734 14.18187 14.38195 14.03364 13.89200
[14,] 14.01044 14.28065 14.04079 14.48845 14.26331 14.20298 14.47237 14.54944
[15,] 13.94350 14.13372 14.25318 14.06951 14.34143 13.97963 14.14123 14.20451
[16,] 14.44115 14.29301 14.49587 14.29923 13.97922 14.12319 14.23661 14.49248
[17,] 14.23711 14.26382 14.26042 14.15493 14.27054 14.45091 14.22829 14.30554
[18,] 14.09667 14.12375 14.33015 14.29663 14.34714 14.42058 14.13269 14.14972
[19,] 14.18734 14.21214 14.30766 14.37810 14.40025 14.34145 14.18464 14.11337
[20,] 14.32253 14.13175 14.28567 14.26828 14.37139 14.34397 14.31214 14.17991
[21,] 14.09459 14.19178 14.19497 14.30854 14.33476 14.11066 14.33767 14.56926
[22,] 14.12338 14.35113 13.93145 14.26679 14.20515 14.26392 14.27445 14.50166
[23,] 14.31364 14.34320 14.40303 13.97131 14.25416 14.39595 14.50251 14.20239
[24,] 14.23567 14.29103 14.31817 13.93823 14.18581 14.21915 14.39891 14.15368
[25,] 14.44172 14.35902 14.00285 14.04830 14.43635 14.29977 13.89981 14.06338
[26,] 14.44096 14.34436 14.31194 14.19296 14.13438 14.22694 14.39332 14.51548
[27,] 14.12326 14.36018 14.29022 14.36724 14.25239 14.36354 14.16247 14.27082
[28,] 14.26235 14.48878 14.19621 14.37071 14.31752 14.37752 14.33697 14.09918
[29,] 14.25471 14.42316 14.28217 14.45604 14.19839 14.23361 14.37846 14.13400
[30,] 14.33200 14.25708 14.19452 14.25667 14.33841 14.45970 14.06224 14.32683
[31,] 14.33106 14.07858 14.50464 14.15687 14.39073 14.15416 14.02893 14.35385
[32,] 14.36448 14.20363 14.43302 14.34439 14.35035 14.35334 14.16553 14.27072
[33,] 14.34356 14.11458 14.33630 14.28756 14.50613 14.09562 14.19797 14.48491
[34,] 14.44336 14.17947 14.40273 14.44520 14.52796 14.46509 14.44792 14.21202
[35,] 14.08786 14.48417 14.13632 14.19586 14.41129 14.24447 14.34218 14.39178
[36,] 14.27113 14.33927 14.35168 14.48763 14.15122 14.28974 14.32567 14.52128
[37,] 14.20669 14.42737 14.18227 14.34127 14.39253 14.21992 14.65543 14.53770
[38,] 14.18332 14.53744 14.38453 14.36447 14.44886 14.41636 14.31806 14.02739
[39,] 14.32899 14.43336 14.67898 14.58960 14.68165 14.47629 14.42268 14.48508
[40,] 14.25231 14.11383 14.28567 14.32668 14.29792 14.33027 14.30024 14.16789
[41,] 14.23932 14.24873 14.26064 14.30223 14.39554 14.35674 14.08204 14.54451
[42,] 14.26181 14.23964 14.33630 14.37623 14.52191 14.34881 14.86752 14.46504
[43,] 14.17040 14.34299 14.47974 14.64284 14.15465 14.39819 14.34947 14.31264
[44,] 14.51404 14.73375 14.32861 14.71923 14.26375 14.41646 14.33325 14.30277
[45,] 14.16284 14.44724 14.41539 14.19196 14.37129 14.27202 14.50018 14.36110
[46,] 14.35880 14.48312 14.44541 14.42165 14.34455 14.43307 14.29931 14.29323
[47,] 14.54298 14.41813 14.13656 14.30296 14.38892 14.52101 14.33747 14.52935
[48,] 14.53616 14.45747 14.41160 14.51872 14.23972 14.34145 14.34738 14.38066
[49,] 14.52124 14.41702 14.79251 14.41449 14.15074 14.27763 14.20735 14.34204
[50,] 14.31017 14.27810 14.15269 14.55246 14.52228 14.44339 14.59160 14.40384
[,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
[1,] 14.32025 14.13070 14.12317 14.21461 14.08478 14.05144 14.22227 14.02326
[2,] 13.97712 14.17287 14.16433 14.42517 14.32537 14.25862 13.96319 14.10877
[3,] 14.01961 14.17478 14.06689 14.16651 14.16980 13.84405 14.10630 14.32098
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[39,] 14.59629 14.25860 14.51459 14.09122 14.18484 14.08159 14.46104 14.59622
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[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
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