Seurat_test BDS3
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Встановлення пакетів
# install.packages('Seurat')
#
# remotes::install_github("satijalab/seurat-data", "seurat5", quiet = TRUE)
#
# BiocManager::install('Seurat')library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(Seurat)## The legacy packages maptools, rgdal, and rgeos, underpinning this package
## will retire shortly. Please refer to R-spatial evolution reports on
## https://r-spatial.org/r/2023/05/15/evolution4.html for details.
## This package is now running under evolution status 0## Attaching SeuratObjectlibrary(patchwork)
# Load the PBMC dataset
pbmc.data <- Read10X(data.dir = "/Users/korshe/bds3_intro_to_r/filtered_gene_bc_matrices/hg19/")
# Initialize the Seurat object with the raw (non-normalized data).
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')pbmc## An object of class Seurat
## 13714 features across 2700 samples within 1 assay
## Active assay: RNA (13714 features, 0 variable features)pbmc.data[c("C1orf185", "TCL1A", "MS4A1",'CDKN2C'), 14:26]## 4 x 13 sparse Matrix of class "dgCMatrix"## [[ suppressing 13 column names 'AAAGAGACGCGAGA-1', 'AAAGAGACGGACTT-1', 'AAAGAGACGGCATT-1' ... ]]##
## C1orf185 . . . . . . . . . . . . .
## TCL1A . . . . . . . . 1 . . . .
## MS4A1 . . . . . . . 36 1 2 . . 2
## CDKN2C . . . . . . . . . . . . .QC and selecting cells for further analysis
Якість контролю даних
# The [[ operator can add columns to object metadata. This is a great place to stash QC stats
pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-")
# pbmc[["percent.mt"]]
mitoch <- pbmc[["percent.mt"]]
mitoch$percent.mt## [1] 3.0177759 3.7935958 0.8897363 1.7430845 1.2244898 1.6643551
## [7] 3.8160920 3.0973451 1.1764706 2.9011786 2.6315789 1.0887772
## [13] 1.0788382 1.4177382 2.3457863 2.3989899 5.9391240 5.0949914
## [19] 1.3961606 1.7076503 1.5282526 3.4700315 2.5906736 1.5426497
## [25] 2.4972046 1.1642950 1.9830028 2.2500000 2.4312896 1.7564066
## [31] 1.8498755 4.5784884 1.9895288 1.7031630 1.9326683 0.6250000
## [37] 1.9195943 2.2262774 1.9867550 2.1892893 2.4848892 1.4388489
## [43] 2.1213407 1.4951627 1.4233242 1.7113095 2.9942966 0.8893830
## [49] 1.0270065 2.2368421 2.4132730 2.7458672 2.4709302 3.1628104
## [55] 2.7864583 1.1096884 3.6617262 2.0896657 2.5719268 1.6519174
## [61] 3.4802203 1.5839493 2.6542056 2.5261638 4.7351525 1.6949153
## [67] 1.3005780 1.9709768 1.5136719 2.1989906 2.6866713 1.4074837
## [73] 2.1982414 1.4099217 5.4054054 2.7739251 2.0018622 2.4468085
## [79] 2.0772947 2.4624625 1.2422360 1.4961726 3.1477927 1.5080113
## [85] 3.6413043 2.4049651 0.9990485 2.1926053 2.6552463 2.1995708
## [91] 1.4102564 2.0876827 1.8666667 1.2532411 2.4686011 2.0817844
## [97] 2.5056948 1.7008986 3.9313262 1.7005196 1.4785609 2.5706010
## [103] 1.7635532 2.4572181 2.6479751 2.3002421 2.2140221 1.7220903
## [109] 2.7202473 0.1245330 2.3565740 1.4471780 1.4014723 1.4983713
## [115] 1.0900474 3.5242291 1.7887088 2.0057307 1.7126546 1.5969339
## [121] 1.8072289 1.5267176 3.9100684 0.9156627 2.4598930 1.8612521
## [127] 2.4737945 3.9041361 0.8273009 5.0349650 2.1878335 0.6069803
## [133] 1.8572258 1.8455860 2.4294156 1.8408551 2.3765996 3.0467900
## [139] 2.0356234 1.9708655 2.9411765 2.3559261 1.3092269 2.2000000
## [145] 1.5714717 1.0315186 1.9283747 1.5657620 3.6002149 2.2649279
## [151] 1.4978602 2.5409836 2.3687327 1.2549914 2.1505376 1.9535375
## [157] 1.9759783 2.2109918 2.1390374 0.8383791 1.6032982 1.8139263
## [163] 0.7299270 2.0051746 1.6050244 2.1209386 2.0683453 3.2773109
## [169] 2.5536261 2.3707606 1.9918515 4.8211509 4.9710025 2.6610644
## [175] 0.5579258 5.2212389 1.6561277 1.9722425 1.5025042 1.7215569
## [181] 1.8847007 1.1682243 5.4612546 0.9235209 3.5838150 2.3902168
## [187] 3.0982368 1.7241379 2.4789291 2.6380068 2.8301887 2.6225279
## [193] 1.7617450 1.8060837 3.1853282 4.4350581 4.4389642 1.4680484
## [199] 3.4688347 2.1729080 1.8726592 6.1705989 2.2266205 1.3009050
## [205] 1.3842746 1.5758372 2.7710258 3.4572169 1.9172829 1.6883117
## [211] 3.1352363 1.0095911 1.8164436 2.0311442 1.0267693 3.1545741
## [217] 1.2732095 2.2817460 1.0154739 1.1568718 4.1295167 2.2845275
## [223] 2.2437308 1.9184652 1.2009238 2.7480205 1.1730205 5.3846154
## [229] 1.6151685 1.6689098 1.4191107 3.2258065 1.2254902 1.7006803
## [235] 1.6205534 2.4793388 2.3749368 3.5856574 1.4791748 3.3526012
## [241] 3.2049625 0.9001637 2.7800491 1.9033675 0.7751938 2.0036430
## [247] 2.1126761 1.4879281 1.1092437 2.8890015 2.7383367 2.4333720
## [253] 1.2589928 3.1337047 1.8844221 2.0599928 0.4408818 2.9177719
## [259] 0.7417710 1.4302154 2.2003474 1.8488746 2.6362039 2.8413028
## [265] 1.5495868 2.2012579 2.6050420 2.7613412 1.0721649 2.5712689
## [271] 2.2930649 2.9979675 3.7426133 2.8892456 5.2694611 2.2258592
## [277] 3.3059846 1.7050068 1.3264129 1.5774648 1.0062893 3.3418295
## [283] 2.0608440 3.0333168 1.6469746 2.7225583 1.4631685 2.5018129
## [289] 2.3918742 1.8297534 1.5750207 0.9351621 1.9902121 2.0489978
## [295] 1.8237082 3.4246575 2.6079870 2.1339656 0.0000000 2.2737405
## [301] 0.8866076 2.2686025 3.0303030 2.0559211 2.2666154 1.6324627
## [307] 2.7038445 2.3126735 1.0747185 1.8570102 3.9051604 2.8702641
## [313] 2.7811366 1.8252934 2.5125628 1.8934911 2.6809651 2.3148148
## [319] 4.1975309 2.2258862 2.4376417 3.8157282 2.2610483 1.3661202
## [325] 2.3513753 0.9866798 1.7505470 2.1698984 2.4096386 1.4925373
## [331] 3.5020936 2.4235080 1.8603466 3.4090909 2.5000000 2.6301269
## [337] 1.8989746 1.5467384 3.1865042 1.3786765 3.7037037 1.6268429
## [343] 1.9204390 4.0144339 2.4602026 2.2471910 1.2369172 1.5005359
## [349] 1.5631601 1.4206788 2.0930233 1.9204390 2.6607539 1.3759611
## [355] 2.3941855 1.3636364 1.7006803 3.0761719 1.6651665 0.5558129
## [361] 1.4981273 1.9821606 2.0820576 1.6465423 1.1217949 2.9126214
## [367] 1.7435897 1.9265722 3.5530381 1.7896476 1.7548258 1.6037736
## [373] 4.0875072 2.0531401 2.1049325 2.2902494 3.2513878 2.2919180
## [379] 2.2648084 5.8425584 2.8713222 1.5625000 0.9196321 3.0834564
## [385] 1.1146497 1.3030888 4.3504532 1.6048144 2.8981507 1.7639903
## [391] 0.1264223 2.3487773 5.6000000 1.2195122 8.0000000 1.1402027
## [397] 1.3999364 2.8711485 2.0191989 1.6276704 1.7030335 2.5510204
## [403] 1.7321785 2.1566402 0.9994448 1.0238908 1.0746085 4.1374474
## [409] 1.3022003 1.7019082 2.0463320 2.9716194 1.8782609 1.2785388
## [415] 3.1002639 4.1955617 4.1480821 3.4318902 2.7147766 2.8417819
## [421] 3.2113518 2.3833671 2.8668610 3.6509350 1.5825492 1.3585917
## [427] 2.6203308 3.5578429 1.9157088 1.9770660 1.5088013 2.1101390
## [433] 3.2435741 1.5057573 4.8218029 1.1874470 1.0029252 1.4485637
## [439] 1.1725293 1.1963023 2.7369826 2.3231802 0.8403361 2.7285130
## [445] 2.5959781 3.1965443 2.2615132 2.0935961 0.9160305 0.9142360
## [451] 2.1946009 1.8552876 2.3754345 1.6582220 3.9519566 1.7455522
## [457] 1.3669065 2.0866774 1.5991471 1.7966361 2.2188603 1.0729614
## [463] 1.4578588 4.2822885 2.5974026 1.6689847 1.4134276 2.5118805
## [469] 1.6696482 2.6777176 1.4184397 1.9521411 2.1897810 1.2509773
## [475] 1.6442451 1.4714205 1.6167380 1.6328332 1.5158270 1.9397441
## [481] 1.9824504 2.0965190 1.4590348 3.7636081 1.8973696 4.4358727
## [487] 2.9547199 2.0632133 3.6175711 1.6386182 3.1250000 1.5978176
## [493] 0.6918574 2.9411765 1.8747142 2.7848101 1.3237519 2.3942538
## [499] 1.6186141 1.1105746 1.0703364 1.1647255 2.2127052 2.7818991
## [505] 3.7674419 0.7950530 2.0519263 0.6644518 2.1551724 1.5345269
## [511] 1.3109978 3.8976149 1.0656197 0.8024072 1.6121153 2.4451939
## [517] 4.4748291 2.4674742 2.1235521 1.8206039 2.1739130 3.2432432
## [523] 2.0176545 2.0879121 1.4756517 1.3748484 1.2918660 1.8573551
## [529] 1.4447236 2.3396880 1.6597510 0.9678534 2.3484435 2.5080906
## [535] 1.4799154 1.6345348 1.2675117 1.2275193 1.8714910 4.8697622
## [541] 1.5511391 2.7848101 3.2105972 0.8771930 1.4527845 1.6651529
## [547] 3.1651830 1.9076305 1.4893617 1.9473081 1.5751790 2.3285899
## [553] 0.7619901 0.9243697 3.3262834 1.8587361 3.5747883 0.7541478
## [559] 3.0877342 0.9447166 2.2935780 1.2265512 2.7143330 1.6284847
## [565] 0.5749880 2.9350105 2.4509804 2.8169014 1.9464720 2.4372760
## [571] 1.1512505 1.7703349 3.3505155 0.5365854 1.8400000 3.6681522
## [577] 3.0479606 2.8742515 2.3330137 1.4414414 3.0525031 0.6107906
## [583] 1.6666667 2.4372230 3.4659820 1.9494585 0.5536627 1.2206148
## [589] 2.5515744 1.6783217 2.0739717 2.4201355 3.3565548 2.2948328
## [595] 1.8978762 2.2279985 2.1606388 2.6887872 2.0297209 1.3873776
## [601] 4.1049031 2.2072937 3.1275720 2.1739130 3.4741144 4.5273632
## [607] 2.1695370 2.1631644 1.8357045 2.6861451 2.0029133 2.6743075
## [613] 1.0638298 1.1344678 1.7790262 1.8485915 2.9234738 2.1276596
## [619] 2.1953279 1.6582220 2.1334544 0.7785888 1.1286682 1.6040330
## [625] 1.8726592 3.0093735 1.6577540 1.6367265 1.3231552 2.9217719
## [631] 2.0418848 2.1664766 1.3761468 1.7326733 3.1237798 2.2808268
## [637] 0.8339651 2.7260926 2.9952077 1.9058732 2.1101993 5.8461538
## [643] 2.1812081 0.6793478 3.4198113 2.3388116 1.2519979 1.2705882
## [649] 2.5277435 2.3760858 1.9548872 2.8387097 1.8097448 2.0931226
## [655] 3.6599099 1.6973812 1.1195159 3.6623648 1.6734280 2.5593728
## [661] 1.4705882 2.8452875 2.0180932 1.7195767 3.3134166 1.4646650
## [667] 2.5857223 0.9174312 1.6976127 2.8955533 2.2339800 3.2879819
## [673] 1.8995929 1.7264276 0.7346939 2.2466040 0.0000000 2.1077283
## [679] 2.0678246 1.7271157 2.6353791 1.6024253 1.4016968 1.8087358
## [685] 1.3058419 1.0362694 3.1451036 1.4857143 1.0152284 3.5060178
## [691] 1.1232449 2.2312373 1.8317503 3.7616023 2.4447031 1.9662921
## [697] 1.5008338 1.1695906 3.6157880 0.7294199 1.1073254 3.3650794
## [703] 1.9213716 1.1932256 1.0512484 1.5850437 2.0931226 1.2340037
## [709] 1.6968326 2.7355623 2.7081244 3.1884058 1.6926202 1.3348589
## [715] 1.9801980 1.9365472 2.0788530 3.1330472 1.9843101 2.8722600
## [721] 2.7235772 3.3377837 1.5360378 1.3458950 2.6357199 2.9423620
## [727] 2.3105360 1.6071429 1.5200517 2.7317073 2.8231798 1.6550988
## [733] 0.8916630 1.5459723 1.7633411 1.3531800 3.5353535 2.6227444
## [739] 2.4408284 2.4578313 0.4066878 2.6058632 1.6269841 1.9679505
## [745] 3.4482759 1.8612521 1.9822640 2.8501629 1.4399206 4.1053447
## [751] 1.2345679 1.7538644 1.5563101 0.9863650 5.1282051 1.4563107
## [757] 0.9150805 2.1681997 2.1287380 2.9475983 3.1789910 2.3218997
## [763] 1.4680971 1.8419777 2.4100995 2.0006669 0.7076923 2.0337013
## [769] 2.6160889 2.4744027 1.3983507 1.5720524 2.2707035 2.1561581
## [775] 1.7200675 2.5909932 0.8782936 2.2094926 1.8875667 2.2736338
## [781] 1.3297872 2.3107715 2.7809965 1.8990073 2.8536199 1.0686395
## [787] 4.5361667 2.9889879 2.0944742 2.8688525 1.3530135 2.0477816
## [793] 1.3684744 4.1967213 1.3377926 1.7918089 1.4044944 3.1604538
## [799] 2.3752013 2.3680931 1.9617706 3.9053254 2.5067144 2.5646950
## [805] 2.8866525 1.8970190 3.5678392 2.3923445 2.0588886 2.9372497
## [811] 1.2597481 2.1987315 3.6156513 2.3802696 1.2866333 1.9173158
## [817] 1.8000766 2.8639618 0.8677897 2.3649728 3.4952607 1.7432647
## [823] 3.2725322 1.9117647 4.7515257 3.3662217 3.4981906 3.1083481
## [829] 2.7114967 1.8104366 3.2544379 1.2845850 1.1411183 1.9314869
## [835] 3.0352304 1.5738499 1.7441860 2.3053892 3.7410926 2.8714107
## [841] 1.9404916 2.5447936 1.0037641 4.7466667 3.0242935 3.8773352
## [847] 1.9820378 1.5325670 2.5450689 2.9232112 1.4492754 2.7529022
## [853] 1.5658747 1.2495778 2.4489796 2.0805666 1.4433920 4.4563280
## [859] 1.1114970 2.0487051 1.8087855 4.0977881 4.9665179 3.6082474
## [865] 2.4758454 2.1002211 1.8393899 2.1841795 2.1254536 1.3289037
## [871] 2.6440038 1.7061611 2.1517554 3.2210835 2.3496890 6.2056738
## [877] 2.2589346 1.5811966 0.6789891 1.2297373 2.4451411 1.0033445
## [883] 1.8079800 1.1413521 2.0508614 1.4413713 2.7732463 3.8567493
## [889] 2.4543081 2.3263225 1.8667525 4.8401421 2.6955950 2.1921341
## [895] 1.4962594 1.7761989 1.2892136 1.9070322 2.9779059 4.8886949
## [901] 2.1723122 2.0287717 4.3815609 3.4782609 0.9819324 2.6405868
## [907] 1.4826375 1.8278302 1.5734266 2.6559865 1.1518325 2.4186047
## [913] 2.3809524 2.3496890 2.9198966 3.1706559 4.0835267 0.8925384
## [919] 2.6072787 0.9781791 2.3354565 2.5882353 2.5956284 3.8719874
## [925] 4.2063492 1.1230219 1.1464968 2.2720388 1.8492834 2.4073182
## [931] 1.5981735 2.1165986 1.0977789 2.7661358 1.2689316 2.4317406
## [937] 2.8094153 2.2767857 1.2211077 2.1044112 1.3608634 1.8456995
## [943] 2.6962926 1.2426422 3.0342156 2.6363092 1.7188189 3.1589339
## [949] 6.5934066 1.4641288 2.8021016 1.5532206 1.6006511 1.8018018
## [955] 1.3101254 2.0103093 3.3602722 2.7144935 1.0780791 1.7454955
## [961] 0.6995885 0.9888752 2.3580299 1.8225585 3.6531365 1.6410256
## [967] 2.4585783 1.8951732 0.7352941 2.5540275 1.8666667 2.4237834
## [973] 2.9636711 4.1428571 1.6363636 3.2301480 1.5885947 1.9635844
## [979] 1.1218766 1.0863005 2.2809124 2.6381284 2.4232633 3.7483266
## [985] 3.4698521 0.4329004 3.7603306 2.5459098 2.3952096 2.8223844
## [991] 1.7954071 2.5260030 2.2566996 1.9789734 1.9213175 1.7714792
## [997] 2.0975832 3.9864865 3.4789987 1.5132085 1.8860189 3.6899314
## [1003] 2.8227914 3.1518625 2.2421525 1.6163793 2.9084158 2.9776084
## [1009] 1.4746544 2.9050279 1.0918675 2.9080119 1.3888889 1.7114914
## [1015] 2.3158694 3.7674038 1.6260163 2.6178010 2.0932445 0.7480131
## [1021] 1.8426104 1.8997197 1.6666667 1.2693498 1.2881065 2.3229462
## [1027] 0.7159905 0.9924110 1.9589107 2.4625624 1.7336776 5.3483462
## [1033] 1.0482965 1.9213175 1.4835605 2.7411592 1.1718750 1.7145505
## [1039] 1.8433180 4.2774566 2.6898048 3.6363636 1.1666667 1.3910355
## [1045] 1.1827957 2.3929471 2.0562029 2.4217221 2.2264631 2.0782396
## [1051] 1.1190550 1.5927190 1.9108280 2.9261156 1.7193566 1.8622628
## [1057] 3.6923077 1.3060761 1.1617100 1.7954229 1.5004413 2.1467603
## [1063] 3.6644951 2.5834230 1.2735327 3.1202435 1.6772439 2.1883548
## [1069] 1.6416346 1.4090909 2.0645536 1.6412661 1.9562474 1.5258216
## [1075] 2.6077098 1.8735363 2.5626424 1.6632017 3.2144430 1.6683023
## [1081] 1.3404826 2.1241830 1.7391304 1.7435897 1.6336634 1.9607843
## [1087] 1.7501716 1.8959913 2.5288002 1.8499486 2.5660964 1.6847172
## [1093] 2.1370207 1.9243986 1.7299578 2.5061125 2.0622042 3.4155598
## [1099] 1.9847328 2.5037556 2.4177566 2.1723896 2.4048096 1.5481651
## [1105] 1.2954659 2.9383430 2.1838035 3.9196472 0.9357720 1.7535314
## [1111] 3.6988111 2.5125628 1.2713548 1.7349063 1.5847861 1.6645327
## [1117] 1.4419611 2.3437500 2.3920266 1.2401353 2.0918071 1.9464720
## [1123] 2.1844660 2.5974026 1.9792648 2.2625448 1.5179393 3.2440056
## [1129] 1.3768686 3.8936959 2.2933588 1.4042868 1.9978402 3.7839248
## [1135] 1.3837638 2.8208745 2.0531401 2.1968616 2.5000000 1.4479638
## [1141] 2.7846028 2.8242075 1.2070566 1.9629226 2.4967990 3.2702238
## [1147] 1.9108280 1.6027875 1.2881679 2.0175892 2.9745809 2.0168684
## [1153] 2.3738872 0.9104704 10.1734104 2.3506366 2.2529442 1.3257576
## [1159] 2.3158870 3.1107045 1.5015974 1.5912481 2.6673640 2.8230185
## [1165] 1.4913658 1.4933059 2.6871401 3.1027254 6.5731167 3.2719836
## [1171] 2.0921771 1.4289967 3.6625245 2.2875817 3.3771107 1.8753168
## [1177] 2.8982036 1.9157088 1.9693654 2.2131427 2.1058965 2.8761062
## [1183] 3.3564393 1.8080210 2.2166022 1.4356436 3.6855037 0.7655502
## [1189] 3.0071077 2.3094688 2.1838035 2.0213157 1.1480833 0.9843660
## [1195] 2.2291022 2.0304569 4.6488625 1.5151515 1.9819044 2.4765158
## [1201] 3.2124352 1.2339056 1.0370370 1.8110795 2.0296643 2.3660068
## [1207] 1.7509728 3.3905967 1.8744142 2.2084463 2.9807343 2.9439036
## [1213] 2.8119508 1.1530398 1.5380151 2.2077452 1.7857143 1.6615654
## [1219] 4.6016823 1.9002375 1.6121153 1.8272787 1.5763829 3.2502226
## [1225] 3.1535793 1.6768293 1.3317665 2.6078710 2.3391813 1.2826183
## [1231] 0.5549390 2.0931072 2.0229008 2.8113505 1.0162602 0.8311688
## [1237] 3.1478770 2.2479564 5.8823529 2.2679325 0.7124352 1.3086150
## [1243] 2.6395939 1.9903498 2.2011006 1.8152696 4.8349057 1.1997177
## [1249] 1.0097087 1.3179572 2.3983316 3.6563877 3.0365203 3.4896017
## [1255] 2.3208880 1.9939577 2.4084778 2.3255814 2.0988310 0.8821676
## [1261] 1.5612490 2.0242915 2.5029240 3.3797217 4.6601942 2.0600559
## [1267] 1.6393443 1.3685551 1.8241347 1.3242994 5.3322395 1.5528860
## [1273] 1.7274472 1.4835420 2.2250210 6.8385650 1.9699812 22.5690276
## [1279] 2.5080906 2.0346320 1.2042819 4.1178153 2.4302430 1.5630551
## [1285] 1.9286754 1.9888992 1.3109978 1.6453382 1.8701870 3.2054951
## [1291] 1.5324421 2.1706956 1.4545455 1.7839923 1.7469561 1.6129032
## [1297] 2.0089286 1.2254902 3.2690696 1.4094687 3.6334913 1.4308426
## [1303] 3.7626628 2.2929936 1.5523285 1.3741135 1.2441680 2.6710403
## [1309] 1.7505470 1.9805420 1.8001800 3.8214406 0.8919722 0.1666667
## [1315] 2.8543783 2.0510483 0.8144021 2.5067385 1.3272658 2.0664506
## [1321] 1.6619790 2.4183417 2.3465704 2.4038462 2.5316456 1.8340211
## [1327] 3.7542662 1.9068459 0.8159565 3.3544878 1.8111965 1.4214047
## [1333] 1.5680927 1.7137564 0.2002002 1.9360787 1.9343066 2.2061943
## [1339] 2.2717149 5.6214866 1.0611050 0.4098361 2.1181717 1.6163793
## [1345] 1.8788163 4.0022548 1.2394958 1.9783325 2.7537372 3.4027222
## [1351] 2.1428571 2.2468354 3.3609352 2.2099448 1.1768448 1.9305019
## [1357] 1.2023217 1.9583070 1.4067278 2.4334383 4.2668735 2.2116366
## [1363] 1.6133098 3.6138358 1.3601236 3.1463031 1.3645224 2.0059752
## [1369] 1.4769765 1.5591398 2.5623505 2.4775737 5.1696284 2.4655709
## [1375] 1.6708438 0.6767644 2.1290752 20.1013514 2.0289229 1.1865211
## [1381] 1.5246015 2.2550226 3.7151703 2.3043036 0.9692373 1.0498688
## [1387] 1.7326733 2.2651934 0.9507347 4.2958129 3.5648995 1.0568032
## [1393] 1.7491254 2.9940120 0.8797654 2.3422251 2.6889535 2.5652174
## [1399] 2.9975430 1.3418903 0.8470090 0.6062443 1.8793274 1.0378058
## [1405] 0.8074283 2.0689655 1.7630465 1.6157989 1.1697861 3.4031414
## [1411] 0.7094486 1.5582488 2.3076923 2.9751488 1.2675419 2.0335986
## [1417] 2.7287319 3.2423208 2.2776107 3.4934498 2.8728348 1.3947001
## [1423] 2.7996071 4.1237113 1.6129032 1.9508389 6.1776062 2.9561201
## [1429] 0.9586276 2.0429009 3.4571429 0.8757526 2.2917693 4.2168675
## [1435] 1.3614405 2.3655914 1.5672616 1.6924565 5.3271028 2.2883295
## [1441] 2.0762712 1.7391304 3.0645161 2.9932546 5.2204176 1.7314189
## [1447] 1.1968085 2.2078621 1.2938230 0.6691201 2.3227384 1.9328586
## [1453] 2.3936170 1.7644006 1.8910741 3.5294118 1.6369764 1.6957606
## [1459] 2.5310411 2.9476463 1.1131725 1.2871287 1.9323671 4.0458530
## [1465] 2.5215660 2.0888889 1.1609287 3.3060668 3.2270916 2.0325203
## [1471] 1.5776699 1.3638187 1.3868252 2.9457364 2.3988439 1.6465863
## [1477] 1.3789581 2.0202020 1.5552100 1.3671090 2.2175732 1.0181618
## [1483] 2.5910627 1.6831109 1.2395042 2.3250853 0.9935205 4.1538462
## [1489] 5.6545314 1.8404908 2.5910931 2.6429010 2.5312686 1.6042781
## [1495] 2.3564065 1.6715831 2.4307371 4.0627886 2.3319366 2.9530841
## [1501] 1.5063731 2.0535159 3.1973075 0.8032129 1.2896480 1.4756517
## [1507] 5.3807947 2.0134228 1.8137255 2.2498803 2.2965552 2.1864212
## [1513] 1.8150879 0.8090615 2.4174328 0.9657594 1.2772586 1.6852936
## [1519] 2.3516836 2.6517968 1.5650297 2.3797468 2.1021021 2.4977698
## [1525] 2.9379157 2.7991387 2.2815159 1.6809492 2.0222447 3.8925652
## [1531] 9.1891892 1.2646370 1.7268446 1.5163002 2.0967742 1.5916149
## [1537] 2.1990741 1.5709156 1.9992003 2.8607756 1.1806375 2.4345709
## [1543] 4.7949162 1.5770840 2.5036343 3.9196472 2.9622980 7.2763029
## [1549] 1.4735432 4.9277825 4.3226553 1.5916575 2.2766079 2.1923269
## [1555] 1.4605203 1.5215554 1.7362394 3.2258065 1.0000000 2.2208122
## [1561] 1.3976555 1.6666667 1.7718371 0.9016072 1.1207970 1.6644175
## [1567] 2.6545002 1.5964523 1.7094017 3.4390113 2.5689460 2.3255814
## [1573] 2.0618557 5.7315234 1.1319112 1.3600302 0.9292929 1.5567087
## [1579] 3.2116788 1.6551309 2.0163831 2.7965284 1.7758047 1.7405063
## [1585] 1.6738903 2.7621195 4.6489564 2.8834356 1.4661274 2.4358130
## [1591] 1.2809564 0.4189944 1.2069736 0.5966587 2.3535851 2.0053476
## [1597] 2.7027027 1.5396459 3.0377266 2.0212228 1.3527575 0.8327025
## [1603] 2.8360414 4.0951123 1.9617706 1.2523315 3.3625731 1.7837235
## [1609] 1.9047619 1.2771392 2.0777480 1.6302463 1.5123740 1.5275505
## [1615] 4.0702314 1.9571295 2.5316456 2.0622725 1.9372077 2.0803443
## [1621] 1.6152717 2.7456647 2.3000000 1.2254902 0.9147609 2.5389222
## [1627] 3.0755712 2.7810886 1.6659547 2.8829455 2.6143791 3.1022782
## [1633] 0.9591116 1.4245014 2.0864947 1.9570011 2.0401224 1.5779703
## [1639] 0.7123776 2.2488756 1.4843321 2.5178903 1.3037810 1.3084112
## [1645] 3.6311239 1.3608528 1.4869888 1.0845007 1.4642550 1.7286367
## [1651] 2.4852845 0.8802817 1.8633540 1.2779553 1.7341040 1.0638298
## [1657] 2.6944586 1.1699507 2.5776053 2.4268380 2.0765737 2.6854802
## [1663] 0.8849558 2.5284900 1.3738551 1.0004350 3.6136662 1.9854133
## [1669] 2.4780785 1.6370603 2.3671897 1.5994668 2.0372011 2.7149321
## [1675] 1.2987013 3.1836271 2.0220588 1.1746522 3.1561059 1.3832659
## [1681] 1.5105740 1.8087855 1.1577424 1.6129032 2.6400285 0.6219765
## [1687] 2.8297581 2.0733062 3.5409556 3.0528476 2.1618081 1.8904321
## [1693] 1.8092610 3.4733441 1.1311417 1.1877395 2.1834061 1.5929690
## [1699] 1.5463918 2.9305913 1.7560074 1.1004449 1.3690816 1.9523937
## [1705] 1.6408962 1.1941619 2.5781502 2.5291048 2.4595469 2.3993381
## [1711] 1.8842530 2.3563456 1.3888889 1.8438490 3.7284895 1.6167665
## [1717] 2.1962617 2.8015821 1.2619669 1.1840689 1.1876485 1.9541779
## [1723] 1.5710383 2.3232323 4.9225160 2.1357380 2.0218579 3.8593063
## [1729] 2.2380468 1.2056044 4.4561572 1.9750520 2.1952359 1.1864407
## [1735] 1.7508754 2.1188201 5.3571429 2.2423664 1.5533981 1.8569088
## [1741] 0.4087890 2.0805369 3.0407524 2.1505376 2.6565465 4.9025770
## [1747] 1.0896483 3.4986714 3.6556604 1.5077821 2.1016431 0.8522727
## [1753] 0.9843660 1.6542597 2.1355617 3.3147551 1.1145273 1.1202140
## [1759] 3.0372757 1.4492754 2.3255814 3.3771290 1.9886364 1.1695906
## [1765] 1.9639935 2.4989040 3.0534351 1.0144928 2.4404086 2.7851459
## [1771] 1.5421115 1.3620072 2.8651015 1.6557734 2.1052632 1.7550858
## [1777] 1.3863773 0.9878419 3.2868217 1.5376730 1.0544074 2.8809704
## [1783] 4.7210300 2.1438217 2.7490542 2.3004695 0.9886488 1.1836735
## [1789] 1.8518519 6.8181818 4.4943820 1.0608856 4.1974480 3.8388626
## [1795] 1.3057671 1.6534392 2.1868050 1.8148820 3.3839479 2.8301887
## [1801] 1.4906027 3.9098741 1.9791292 2.4087850 1.8011527 2.3609817
## [1807] 1.1296076 1.4091123 1.0240655 2.7522936 2.6219192 2.9475983
## [1813] 2.1714922 0.4990403 3.9145907 1.6242156 1.9280206 2.8892456
## [1819] 2.6067665 2.4913094 3.2159930 1.7894299 4.3678161 0.9379509
## [1825] 1.1208577 3.3692254 1.9833948 2.3312883 2.1350260 1.2006861
## [1831] 2.3148148 4.8685783 0.7874016 1.5097691 3.8213628 2.4209486
## [1837] 1.2328767 1.6265060 1.0939511 2.8058361 2.2664835 3.2554257
## [1843] 3.0647553 2.5806452 2.8562049 1.9820972 1.3734467 1.6068759
## [1849] 2.7210884 1.5825620 1.4877790 1.1717545 0.9463722 2.0111732
## [1855] 2.3394724 1.5971149 2.1188201 2.1926053 1.9326339 1.7358491
## [1861] 1.3638039 1.8348624 3.1204291 1.6436903 1.5683814 3.0249110
## [1867] 3.1804281 2.3157895 1.9443614 2.1482730 1.7712177 2.2315653
## [1873] 1.5812994 3.2527881 2.4390244 2.2168675 1.3337038 1.7586240
## [1879] 1.1801731 1.4956163 1.2173913 2.7154441 3.0337079 1.6783763
## [1885] 1.0804769 2.5924352 3.5842294 2.1017699 0.6024096 1.4250956
## [1891] 1.3389441 2.4174981 1.7575484 0.7137193 2.0525060 0.7103394
## [1897] 0.6666667 1.7055145 1.6717325 1.4939759 3.3626487 3.1627133
## [1903] 1.6113744 0.5343198 1.6885553 1.8787879 2.0861074 1.9061166
## [1909] 2.5005788 1.8702513 2.2648084 4.3142305 2.6301664 2.3444976
## [1915] 1.2583893 2.0719312 1.6917293 2.2707424 1.7107309 1.7538162
## [1921] 1.9674936 3.2349603 1.0711553 2.7728873 2.3694391 1.8666667
## [1927] 2.3876404 3.4555712 2.0828228 2.4498886 1.5859408 1.0576352
## [1933] 2.5723473 2.5837989 1.8465326 3.3467742 1.6357206 2.0717829
## [1939] 1.5254237 1.9507187 1.6556291 3.1598513 0.6782216 2.1803182
## [1945] 0.9137636 1.7479971 1.4522822 2.3298143 2.8320312 2.6200873
## [1951] 3.0211480 1.9607843 1.5613383 1.2377139 1.8541409 2.0570670
## [1957] 1.1301800 2.8289756 1.2017167 2.4793388 1.4359352 1.2007685
## [1963] 1.7216643 1.6868740 2.0138889 2.0905923 2.4563319 1.0195759
## [1969] 2.2610922 1.7916390 2.4377318 1.6136687 2.0833333 0.8374384
## [1975] 2.1108179 2.8985507 3.5795197 2.5507794 1.6042781 1.6595745
## [1981] 1.8393624 2.4701195 2.8144744 2.6033058 2.8050491 1.0956175
## [1987] 1.9722098 3.3836858 0.4188482 2.4404762 4.1504540 3.2231742
## [1993] 2.7244218 2.2231371 1.7150858 1.7619252 1.5586946 2.3560209
## [1999] 0.8638211 2.7577938 1.9719544 1.7027864 3.0281439 1.4338973
## [2005] 1.4204545 2.9933481 2.1276596 1.7916207 1.8621974 6.6787004
## [2011] 2.4207746 3.2112845 0.6637168 1.0348071 2.4337867 2.9869322
## [2017] 0.6868132 2.9622063 1.8827327 1.1704462 1.3274336 1.1711712
## [2023] 2.7865881 1.2528474 2.5295110 2.2180274 2.0645161 1.9650655
## [2029] 1.6490278 2.8791926 2.1095890 1.3550136 10.4477612 0.9654063
## [2035] 1.5303430 2.1172381 2.0091324 2.4472169 0.9349435 2.6589595
## [2041] 1.6938899 1.8081366 2.4571854 0.8970976 3.2236842 2.2719077
## [2047] 1.8813314 1.6675088 2.7428571 2.4441341 2.0486267 1.6037736
## [2053] 2.0955166 6.0080107 0.8420010 5.0509956 2.2641509 1.9587083
## [2059] 2.6971802 1.6237494 3.5277178 2.6755180 0.5938785 1.7554479
## [2065] 4.3365134 1.6081871 1.8953440 2.1319121 2.2213855 0.9483667
## [2071] 1.9451813 1.0696404 1.9531250 0.4241782 2.1544715 2.5247971
## [2077] 1.9671074 2.2481266 2.2709777 2.2095960 1.8686131 1.0657194
## [2083] 1.5170670 1.9164619 1.5636634 1.4524328 1.7672151 1.1011011
## [2089] 1.9480519 1.3439522 2.1761658 2.1425789 1.4189988 2.0198562
## [2095] 1.4480409 4.0625000 2.6355047 1.9442985 3.0139451 3.7593985
## [2101] 2.1318790 1.5533981 5.4302423 0.9556314 1.5781923 1.2669288
## [2107] 2.2911526 2.0620543 1.1592958 2.2325020 2.5000000 1.5843430
## [2113] 2.1345029 1.3498920 3.2184950 2.7104137 3.3333333 2.7687776
## [2119] 2.9356061 1.5540296 0.9557945 1.9710283 1.4459665 2.1721959
## [2125] 2.8387097 2.2003929 1.6048144 1.6957862 3.2846715 2.3017903
## [2131] 3.2102729 3.5537562 1.6656385 3.6895977 1.7857143 1.2826087
## [2137] 1.5022861 3.0962748 2.3174157 3.7068598 2.7787674 1.8573551
## [2143] 2.0070518 1.7226148 1.8451845 2.7445461 2.3571429 2.7876631
## [2149] 10.4602510 0.8015087 0.6106870 3.1592887 2.1012931 5.3595658
## [2155] 2.2480058 1.7341040 5.4634146 1.4962121 1.6371534 1.9111570
## [2161] 1.4184397 2.5279248 1.4170040 3.1224322 2.3105857 1.4907807
## [2167] 0.9270705 3.7333333 1.6939891 1.5625000 1.3008812 2.8491031
## [2173] 1.3911182 2.9464286 1.1590470 1.8154312 1.8628617 1.5436242
## [2179] 1.5694481 1.8090452 2.7647059 3.2003085 1.6422287 1.9399249
## [2185] 4.1509434 1.2233802 2.3572076 1.3129103 2.1252154 2.0496894
## [2191] 3.3736153 1.0026996 2.0110957 3.4547739 2.2167488 1.2360212
## [2197] 2.6362039 2.2350993 2.0319303 1.4831717 1.3282732 2.2114109
## [2203] 2.9018885 2.2166247 4.8971596 1.2531328 1.7383746 2.2522523
## [2209] 1.1550152 1.2692967 2.6901670 2.9859485 3.0912659 1.8489985
## [2215] 0.7751938 1.7159763 1.3561511 1.2073272 1.4643075 2.7647366
## [2221] 2.1880065 2.0475020 3.6664992 3.8665254 3.0127462 1.8937253
## [2227] 2.4660912 1.8134034 1.9057893 2.1276596 0.8278146 1.8641010
## [2233] 3.0551009 2.0256181 0.0000000 1.6967126 3.5358114 3.5946081
## [2239] 1.5561960 1.5349887 4.8879837 2.1954162 4.3099025 1.6443988
## [2245] 2.4424995 2.3797468 1.5643803 1.8238434 3.3992897 1.4932338
## [2251] 1.4374701 3.1524123 5.5124224 1.4897579 2.7397260 2.5033829
## [2257] 2.6031746 2.5171625 2.4106759 1.3640239 2.4894068 1.2786762
## [2263] 2.0655738 1.0355030 2.5771812 3.3503277 1.1851016 2.3244313
## [2269] 2.4775962 2.5502550 1.8187067 2.9624277 1.6500516 0.8347979
## [2275] 3.8509317 4.8913043 2.1022456 3.0769231 1.8925519 1.8117543
## [2281] 0.9057971 2.4240232 1.4959724 1.8077239 1.0144928 2.7647610
## [2287] 3.2158078 1.9575856 3.3872209 1.5897635 1.6638935 2.1579322
## [2293] 3.4995626 3.6150235 2.5678119 1.9464720 1.8894332 0.6188119
## [2299] 1.2564991 1.9145803 1.4811276 1.0993177 2.6996625 2.0392157
## [2305] 3.0097499 1.2368584 2.5953220 1.8957346 2.6816945 1.2516764
## [2311] 2.2241232 2.7427724 1.3525699 1.3766325 2.9812054 1.5947467
## [2317] 0.6839277 2.5133522 0.7323569 2.2461815 1.0033445 1.6059538
## [2323] 1.7628205 2.1393035 1.0622155 1.9894311 3.5444509 2.4180034
## [2329] 2.0903955 2.0987654 5.2464229 1.4560280 1.6319130 1.7452007
## [2335] 0.8797654 2.6288660 0.7838746 2.6522001 2.1676301 1.6923656
## [2341] 1.0370961 2.2020725 2.3754789 1.4726185 1.0236220 3.1905196
## [2347] 4.3303929 1.5962164 2.2192334 2.4420402 3.3371692 1.3687601
## [2353] 2.1369863 1.1820331 1.0778443 2.3738872 2.8070175 1.8653987
## [2359] 7.6318743 2.3832221 1.7722879 1.7710310 1.1348006 1.1695906
## [2365] 1.4288266 1.5209125 1.7463235 3.1336088 7.2642968 1.2488437
## [2371] 3.6832413 1.6057935 2.6521739 1.2738854 1.7867113 1.6926739
## [2377] 2.4878049 0.8759124 2.2638564 3.7138176 1.3325257 1.6829052
## [2383] 2.9442692 1.6926202 1.2118986 2.0683453 3.3496732 2.5069638
## [2389] 1.9591611 2.1997360 2.4813154 2.6134801 1.4423077 2.0216103
## [2395] 2.5587467 2.1107129 6.0755337 1.9230769 2.3886082 1.7374517
## [2401] 4.5327103 1.9205298 1.1117287 2.4440978 1.4238411 1.6103896
## [2407] 1.7156863 2.9679922 0.8819018 2.2191401 0.4694836 1.6533637
## [2413] 2.1645022 1.9641542 0.9027987 1.9105200 1.3634427 1.5734266
## [2419] 1.3242454 3.9669421 6.5104167 2.0413064 3.2833021 5.4216867
## [2425] 3.3282905 4.0381992 1.8464529 2.8619529 2.4727273 1.9136808
## [2431] 2.1445592 1.7900339 1.8210198 1.3280212 1.5349887 2.3409894
## [2437] 1.2740934 1.7247210 4.5945946 2.4416712 2.6780627 3.6333412
## [2443] 1.2573964 3.6697248 1.3181019 2.9838022 1.8295404 2.3157895
## [2449] 1.5011547 1.8064516 1.3834693 2.9126214 1.8213866 1.6941102
## [2455] 2.8048780 1.6129032 1.7470074 0.7541478 1.2833676 1.3742556
## [2461] 1.2186380 3.2511611 2.2093635 2.4796922 3.2462950 2.2988506
## [2467] 2.0270270 1.8987342 1.9446845 1.2820513 2.3510972 1.7992424
## [2473] 2.8355388 2.1921341 2.7706890 2.4313372 1.7348609 2.5471698
## [2479] 2.9434547 3.4136546 1.4171512 2.4568740 1.1466296 3.5499571
## [2485] 2.4286582 2.9993183 2.4788392 1.3464526 1.8705036 2.3547881
## [2491] 3.1333690 1.7146356 1.4889091 8.8141026 0.9930487 1.2687970
## [2497] 2.3741690 1.3949433 0.9735202 2.2045315 6.4578500 1.8996960
## [2503] 2.5703794 2.5536854 5.9650824 2.6041667 1.9379845 1.4129737
## [2509] 1.4198128 1.8469657 1.9649722 1.5524806 2.8317601 1.1202830
## [2515] 1.1711712 1.8138425 2.0539670 1.9567456 10.1405622 0.5845817
## [2521] 2.1464163 1.6636528 2.9991431 1.4373717 1.4107884 1.6710821
## [2527] 3.1523643 2.4810964 2.7229299 2.0857930 1.3999517 3.4926471
## [2533] 1.3527054 3.2454361 2.1320495 2.1871821 3.1849439 1.9857808
## [2539] 2.7805865 1.5498870 1.5759850 2.3712183 3.1585597 2.0447907
## [2545] 0.7231405 2.9585799 3.8843722 2.6776519 1.7688679 3.3149171
## [2551] 6.6889632 1.8475073 3.0721966 3.0205397 3.4443817 2.7384756
## [2557] 1.9214703 2.9572837 1.5696784 2.1938572 3.3057851 1.0140029
## [2563] 3.2947462 1.4221073 1.7341040 2.2093635 2.7600849 1.7662066
## [2569] 2.5906736 2.4850895 2.1184778 1.7254902 1.7241379 3.3492823
## [2575] 4.3460765 1.5144959 2.0952381 1.8653690 4.3135912 2.3647112
## [2581] 1.6871705 3.1089978 3.4358047 1.5706806 3.0225783 2.4235430
## [2587] 4.0236686 2.4723830 3.1922440 2.7863777 1.8238994 2.2063595
## [2593] 2.1958607 1.3131715 2.4478331 2.4664377 2.3909396 1.1939070
## [2599] 2.3900574 2.0123839 2.6136364 2.3553163 1.9806153 5.5405405
## [2605] 1.6229713 2.8164117 0.9501188 0.5908419 3.6755387 0.9730208
## [2611] 1.7347308 2.2614028 2.8648649 2.3976024 0.8611955 1.1639185
## [2617] 1.7713366 1.4636696 1.8518519 1.4476190 3.8287154 1.2333966
## [2623] 1.3225569 1.6414141 2.9751063 3.2608696 2.9580153 2.3056653
## [2629] 1.8043685 0.3868472 1.2358393 2.2959184 1.6519824 2.6938478
## [2635] 1.5191200 2.8595458 1.1613438 1.6080402 1.3131313 2.8812057
## [2641] 2.0018408 1.3237064 1.2359985 1.0271703 3.5697057 2.8391167
## [2647] 1.4830508 1.6925892 2.1225471 0.7194245 1.8898932 2.2413793
## [2653] 1.4899713 2.4059493 1.6650809 1.7386985 1.3388260 2.6636225
## [2659] 2.9103215 2.4440240 1.0442566 1.7587940 4.9938348 1.7227235
## [2665] 2.1376434 1.9821220 2.2692109 2.0592021 2.4089307 1.1767531
## [2671] 2.4042074 2.8683915 2.1124104 2.8483920 1.7429938 2.5336927
## [2677] 1.9118428 3.7760417 1.3728964 2.2248709 2.6241799 1.8382353
## [2683] 1.3547841 2.2875817 1.1002445 2.1160289 2.3220596 1.3047024
## [2689] 1.3261297 1.5168539 3.4313725 2.4546425 1.8925057 0.6858711
## [2695] 1.3019080 2.1104365 0.9294220 2.1971496 2.0547945 0.8064516mitoch$sum <- mitoch$percent.mt + 10head(pbmc@meta.data, 5)## orig.ident nCount_RNA nFeature_RNA percent.mt
## AAACATACAACCAC-1 pbmc3k 2419 779 3.0177759
## AAACATTGAGCTAC-1 pbmc3k 4903 1352 3.7935958
## AAACATTGATCAGC-1 pbmc3k 3147 1129 0.8897363
## AAACCGTGCTTCCG-1 pbmc3k 2639 960 1.7430845
## AAACCGTGTATGCG-1 pbmc3k 980 521 1.2244898meta_data <- pbmc@meta.data
pbmc@assays$RNA## Assay data with 13714 features for 2700 cells
## First 10 features:
## AL627309.1, AP006222.2, RP11-206L10.2, RP11-206L10.9, LINC00115, NOC2L,
## KLHL17, PLEKHN1, RP11-54O7.17, HES4VlnPlot(pbmc, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3)
VlnPlot(pbmc, features = c( "percent.mt", "nFeature_RNA", "nCount_RNA"), ncol = 2)
VlnPlot(pbmc, features = c( "percent.mt"), ncol = 2)
1 - мітохондрії 2 - унікальні гени 3 - кількість підрахунків цих генів
plot1 <- FeatureScatter(pbmc, feature1 = "nCount_RNA", feature2 = "percent.mt")
plot2 <- FeatureScatter(pbmc, feature1 = "nCount_RNA", feature2 = "nFeature_RNA")
plot1 + plot2
pbmc <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5 )
# pbmc
pbmc2 <- subset(pbmc, subset = nFeature_RNA > 200 & nFeature_RNA < 2500 & percent.mt < 5 & nCount_RNA < 5000 & nCount_RNA > 1000 )& - і | - або
Normalizing the data | нНомралізація даних
pbmc <- NormalizeData(pbmc, normalization.method = "LogNormalize", scale.factor = 10000)
pbmc <- SCTransform(pbmc)## Calculating cell attributes from input UMI matrix: log_umi## Variance stabilizing transformation of count matrix of size 12519 by 2638## Model formula is y ~ log_umi## Get Negative Binomial regression parameters per gene## Using 2000 genes, 2638 cells##
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|======================================================================| 100%## Calculating gene attributes## Wall clock passed: Time difference of 27.02532 secs## Determine variable features## Place corrected count matrix in counts slot## Centering data matrix## Set default assay to SCT# pbmc@assays$SCT@data
sct_mtrx <- as.matrix(pbmc@assays$SCT@data)
raw_mtrx <- as.matrix(pbmc@assays$SCT@counts)
sct_mtrx[10:15, 1:5]## AAACATACAACCAC-1 AAACATTGAGCTAC-1 AAACATTGATCAGC-1 AAACCGTGCTTCCG-1
## C1orf159 0 0.0000000 0.0000000 0
## TNFRSF18 0 0.6931472 0.0000000 0
## TNFRSF4 0 0.0000000 0.0000000 0
## SDF4 0 0.0000000 0.6931472 0
## B3GALT6 0 0.0000000 0.0000000 0
## UBE2J2 0 0.0000000 0.0000000 0
## AAACCGTGTATGCG-1
## C1orf159 0
## TNFRSF18 0
## TNFRSF4 0
## SDF4 0
## B3GALT6 0
## UBE2J2 0raw_mtrx[10:15, 1:5]## AAACATACAACCAC-1 AAACATTGAGCTAC-1 AAACATTGATCAGC-1 AAACCGTGCTTCCG-1
## C1orf159 0 0 0 0
## TNFRSF18 0 1 0 0
## TNFRSF4 0 0 0 0
## SDF4 0 0 1 0
## B3GALT6 0 0 0 0
## UBE2J2 0 0 0 0
## AAACCGTGTATGCG-1
## C1orf159 0
## TNFRSF18 0
## TNFRSF4 0
## SDF4 0
## B3GALT6 0
## UBE2J2 0