Get data to use as input clustering algorithms

getClusterInputData(inSCE, inputData, useAssay = "logcounts",
  reducedDimName = NULL)

Arguments

inSCE

Input SCtkExperiment object. Required

inputData

A string ("Raw Data", "PCA Components", "tSNE Components", "UMAP Components")

useAssay

Indicate which assay to use for PCA. Default is "logcounts"

reducedDimName

If clustering on PCA, t-SNE or UMAP data, dimension name. The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>.

Value

Cluster input data

Examples

data("mouseBrainSubsetSCE") getClusterInputData(mouseBrainSubsetSCE, "PCA Components", useAssay = "logcounts", reducedDimName = "PCA_logcounts")
#> PC1 PC2 PC3 PC4 PC5 #> X1772063061_G11 -4.965731 10.97920765 -0.04381621 2.3068016 -4.13081305 #> X1772067064_C10 -18.890459 0.95582759 5.31525459 -9.1213043 1.86047705 #> X1772062113_D09 -18.406337 -3.35364459 -1.19246897 0.1815060 0.35969359 #> X1772062111_A12 -5.346435 7.30229940 0.24126610 4.0555017 -5.52526581 #> X1772071040_C12 -14.947400 -6.29704591 -3.87563734 1.2613889 0.24360568 #> X1772062111_D09 -13.036536 2.49172224 -2.39756692 2.7622812 -0.73069361 #> X1772071036_G02 -15.135144 -5.69158577 -7.12771211 -9.8061361 -0.04520559 #> X1772071040_D04 -18.895752 -0.13970711 4.49116731 -4.0520267 0.17992464 #> X1772058177_E12 -16.116131 3.03765472 8.24081041 3.4103398 6.93360097 #> X1772066070_G10 -8.319605 -4.12938938 -8.00468997 1.4153245 0.82968886 #> X1772063074_G10 -8.762477 7.99766373 0.46147136 0.1289979 -4.76251207 #> X1772062115_E07 -7.856956 9.71649024 1.53772839 3.8540320 -4.20323457 #> X1772062109_F01 -18.406307 -2.80346040 6.39909802 2.9335727 2.34379762 #> X1772060226_G05 -6.366600 3.86306754 -6.64012612 2.0960110 -2.96416946 #> X1772066108_D06 -16.058035 -3.23126503 -2.71698429 0.3196868 0.39365104 #> X1772060224_F07 13.545249 -8.10304325 -1.29371573 1.8977882 0.37560254 #> X1772062111_F12 13.596193 -0.14121334 6.80294227 0.6920214 -1.93829672 #> X1772063078_G02 9.630331 -10.75476957 -4.19167018 4.6743298 -3.58888150 #> X1772060240_H11 10.634146 -0.06744365 -6.50560100 2.6145418 7.09649509 #> X1772067094_C07 17.348662 6.90639608 0.90650306 -5.4277854 1.88967137 #> X1772058177_A09 12.299035 1.40306010 -12.15151103 -2.1500178 4.21632753 #> X1772058171_C05 17.326062 -2.37454887 9.97482132 -5.4041548 0.07678323 #> X1772062128_B03 14.507342 7.14843693 0.38287054 -7.6066871 0.68959728 #> X1772062118_F04 14.638151 -2.69166061 -0.78582080 0.6690898 -2.87377949 #> X1772062109_E05 10.977607 1.53314470 3.10007348 8.4871111 3.45841047 #> X1772062128_D02 2.456726 -18.37327147 8.33368108 1.9893804 2.64506331 #> X1772062109_E12 14.919914 -2.59068282 2.20343861 -0.1740233 -4.25590463 #> X1772062113_E05 12.167693 -6.33849122 -3.37764459 -3.1656949 -6.81112645 #> X1772062128_F05 12.211071 9.28909769 -2.46810592 1.0068099 11.26304464 #> X1772062118_D09 15.251722 4.45715439 4.38194462 0.1513139 -3.02555193 #> PC6 PC7 PC8 PC9 PC10 #> X1772063061_G11 4.5181980 -2.352091298 4.4318425 -0.04017713 -0.8166941 #> X1772067064_C10 0.4807260 -3.512436746 -0.9723091 0.27062621 -3.8061248 #> X1772062113_D09 -3.8395994 -4.924280548 -0.5400708 1.64252082 -6.1456179 #> X1772062111_A12 -0.4592041 1.528288490 -7.3189711 -3.03619068 1.6438337 #> X1772071040_C12 3.4971041 5.137980042 -3.2682743 -5.21257502 4.5369576 #> X1772062111_D09 0.2575463 1.964380321 -0.3976526 -0.10622474 1.5228929 #> X1772071036_G02 0.9338416 -0.529926721 -1.3958379 0.93166281 2.0397167 #> X1772071040_D04 -0.4627881 -0.953284136 -1.8834822 -2.97116796 0.2673850 #> X1772058177_E12 -3.6599700 7.007138661 8.2351445 -0.73413511 0.8234591 #> X1772066070_G10 -0.3323437 4.962404399 1.1179523 -0.67573149 6.5551307 #> X1772063074_G10 1.8254195 -2.065692758 -0.4047944 1.36889410 1.8198757 #> X1772062115_E07 5.1286187 0.006007208 0.7823396 3.12684843 1.9144043 #> X1772062109_F01 -5.0623924 0.306877841 -0.6898370 -0.34881706 -0.7234280 #> X1772060226_G05 2.6569195 -1.262483960 3.9734049 4.85819154 -4.5201566 #> X1772066108_D06 -5.2174554 -3.524140636 -0.7625122 2.30756275 -0.4850380 #> X1772060224_F07 -4.1296245 3.681341784 2.3306414 4.00798488 -1.7266547 #> X1772062111_F12 1.9998365 -2.161803203 1.4077655 -12.61183203 -4.8279031 #> X1772063078_G02 -4.1741575 -1.128363092 2.1834320 -3.14679781 0.9376355 #> X1772060240_H11 -1.9251076 -5.091252385 -0.3239583 -3.23036723 -0.4138460 #> X1772067094_C07 -1.7875373 0.161880566 4.5933664 0.87227462 2.2820255 #> X1772058177_A09 2.5652065 0.344147168 -2.0239076 -1.18528308 -4.4824626 #> X1772058171_C05 -3.3265740 -4.279245888 -2.7330513 2.75462363 7.3674694 #> X1772062128_B03 -0.4798581 12.285782624 -2.3185883 0.51560042 -5.0584168 #> X1772062118_F04 0.6240584 -0.575693909 3.2438626 1.93179726 0.4726490 #> X1772062109_E05 -3.6042380 0.387171172 -7.0503817 4.00528346 -3.1344517 #> X1772062128_D02 13.1876630 0.512188981 0.7544335 3.37642887 -1.5963468 #> X1772062109_E12 0.6386178 1.246832326 -6.8945591 2.14085085 -0.3074912 #> X1772062113_E05 -2.3899758 -1.770356911 4.8263134 -1.15392722 0.8629560 #> X1772062128_F05 4.5155591 -4.833113274 -0.7073797 -0.21883187 4.2216046 #> X1772062118_D09 -1.9784891 -0.568256120 1.8050690 0.56090778 0.7766365 #> PC11 PC12 PC13 PC14 PC15 #> X1772063061_G11 -3.2480903 0.9487083 1.27937637 3.09424250 -4.52757992 #> X1772067064_C10 -0.8068832 -0.5064253 3.53509178 2.39974704 0.37367346 #> X1772062113_D09 2.8357825 -2.2555475 -0.03669704 2.06258977 0.06230273 #> X1772062111_A12 -3.4035326 -4.9864196 3.48565686 -0.06059316 6.63120899 #> X1772071040_C12 4.0619662 2.8074414 1.06747423 -0.44814272 -0.48941197 #> X1772062111_D09 1.5509194 -0.0180525 -6.45763178 -0.44470440 -5.24105898 #> X1772071036_G02 -4.2322725 2.2313385 -2.62220651 1.55990123 1.97731270 #> X1772071040_D04 -0.1555567 1.2167777 2.61652045 0.10127887 -3.12106722 #> X1772058177_E12 1.8686413 -4.0013622 -1.61532970 1.96583784 3.28427346 #> X1772066070_G10 -4.3743186 -0.2074400 -0.58992815 0.13263314 0.33115840 #> X1772063074_G10 1.5560468 -3.6989930 -0.23234252 1.54967143 0.57580978 #> X1772062115_E07 1.1520380 1.6306453 1.38975004 -3.24886099 -4.37186880 #> X1772062109_F01 0.8750064 0.5717342 -0.74856749 -1.84525895 -1.06002090 #> X1772060226_G05 1.7061330 4.6379660 -4.83858202 -2.65759405 3.91743393 #> X1772066108_D06 -1.5493684 1.0628486 1.32197634 -4.23128288 1.92415012 #> X1772060224_F07 -0.1038218 -1.3264683 0.89016733 6.07978135 -3.96417135 #> X1772062111_F12 -1.1953543 1.7541993 -4.32323904 -1.09721710 0.29881613 #> X1772063078_G02 0.5655448 0.9752864 1.54686995 -0.02971371 0.44095431 #> X1772060240_H11 -4.9790550 1.4414373 2.23469245 0.87843878 -5.07754477 #> X1772067094_C07 -7.2084978 2.0472448 -3.49945837 -0.59383140 3.59792576 #> X1772058177_A09 2.8905681 -9.6840053 -3.38586087 -3.93134326 -0.70638296 #> X1772058171_C05 2.8335589 -2.2862203 -3.72477723 -5.19606524 -3.29420506 #> X1772062128_B03 1.5717964 3.2405388 3.82010918 -2.76417994 -2.01830624 #> X1772062118_F04 -2.6727961 -4.4932716 6.71965111 -1.66387443 -1.32690633 #> X1772062109_E05 -2.2586413 5.0341578 0.12245043 -2.81348145 1.61494190 #> X1772062128_D02 -2.3765878 -1.0329618 0.51560543 -1.69737806 1.84460046 #> X1772062109_E12 1.1215922 0.5665380 -4.73060554 9.23296588 0.26590050 #> X1772062113_E05 7.3994142 3.4637767 3.19103015 -0.75780265 2.70148973 #> X1772062128_F05 6.4025100 2.7683481 3.05542371 3.59612475 3.34440447 #> X1772062118_D09 0.1732583 -1.9018198 0.01338046 0.82811181 2.01216765 #> PC16 PC17 PC18 PC19 PC20 #> X1772063061_G11 -4.37328114 -3.61496569 3.82603057 3.67065121 1.46105538 #> X1772067064_C10 -3.12287499 2.97688219 1.08441432 -2.39303041 1.22517982 #> X1772062113_D09 0.01345706 -3.73095265 -2.27597338 3.80869625 -2.37018306 #> X1772062111_A12 2.20489653 -1.74910249 -2.74551187 0.34915233 -3.01377849 #> X1772071040_C12 -6.49852050 -3.26117489 -0.85379498 -0.46781636 -2.43670575 #> X1772062111_D09 4.09607891 3.18098552 -4.58301365 2.61598478 -1.02495217 #> X1772071036_G02 1.96606692 -0.06799002 0.34574889 -5.64462412 0.97177646 #> X1772071040_D04 -2.60587898 5.38044910 -0.59534289 1.39595661 -4.15915619 #> X1772058177_E12 -2.38296879 -1.65867555 -1.42951475 -2.49253300 2.69000177 #> X1772066070_G10 1.47325534 1.44765098 3.87898259 1.34175711 3.00106130 #> X1772063074_G10 4.98651621 -1.62205581 2.64943094 -3.43414865 -1.87200028 #> X1772062115_E07 0.45029243 4.04237592 -2.00553170 -1.84399226 1.74302243 #> X1772062109_F01 2.91632344 0.05819949 -0.08499291 -0.50528593 2.33620485 #> X1772060226_G05 -1.60121912 -3.28527728 1.20102637 -3.50767900 -2.65222683 #> X1772066108_D06 2.53159631 -0.57338456 3.63181030 6.32457881 3.78779308 #> X1772060224_F07 3.32662901 2.39544663 2.95654773 -1.86974989 -5.75342456 #> X1772062111_F12 3.47732549 0.90578301 3.36506574 -1.61354479 1.29071109 #> X1772063078_G02 -2.79386368 0.74116590 3.84347836 0.88413663 -2.69308089 #> X1772060240_H11 1.20164637 -5.52477314 -6.06637198 -2.92457455 0.67241931 #> X1772067094_C07 -2.05138742 2.25964558 -3.66427536 4.51732811 -3.29333082 #> X1772058177_A09 -3.43477144 3.29535000 0.70825097 0.43275947 1.19310680 #> X1772058171_C05 -1.50460617 -4.69017776 2.18001688 -1.02676875 -1.15019341 #> X1772062128_B03 3.07120493 -3.90764535 1.08879371 2.00799470 -0.04340518 #> X1772062118_F04 -0.68752386 0.43321125 -0.58860654 -2.56238842 3.46789626 #> X1772062109_E05 -3.41142002 3.64689773 0.72408136 -3.36179046 0.79183019 #> X1772062128_D02 2.10533646 -0.91055652 -1.62095904 2.44209000 -1.00946888 #> X1772062109_E12 -2.21748309 -0.63078708 -1.20546160 1.93465921 5.96133943 #> X1772062113_E05 1.35104985 1.95152723 -5.38955357 0.13074522 3.01739618 #> X1772062128_F05 3.17115856 1.40898230 2.66468219 1.69620651 -0.56544262 #> X1772062118_D09 -1.65703462 1.10296597 -1.03945671 0.09522964 -1.57344521 #> PC21 PC22 PC23 PC24 PC25 #> X1772063061_G11 1.7953576 -0.8347339 -3.4564900 -5.42732156 2.1029716 #> X1772067064_C10 0.7953070 -0.3314923 -4.0370875 5.04133420 -0.2980030 #> X1772062113_D09 1.7523746 -0.2177483 1.9815322 -0.26975253 -2.6135076 #> X1772062111_A12 1.5615554 2.7419712 -2.4095973 -0.77863276 3.1681143 #> X1772071040_C12 0.4247356 3.1737253 -0.2498618 0.72277381 -4.2389881 #> X1772062111_D09 -2.8883891 -0.1518347 -0.5497095 0.01854186 3.6275209 #> X1772071036_G02 -3.6839208 1.0386541 -1.5342645 -5.38472423 0.8593105 #> X1772071040_D04 0.6423257 -1.9078461 6.2334284 -0.69453900 4.3807340 #> X1772058177_E12 -0.2399918 -0.6376112 0.5701916 -0.40048126 2.1345250 #> X1772066070_G10 5.0077584 -3.2772440 0.4255412 4.23250398 0.5854020 #> X1772063074_G10 0.6741411 -6.7548338 3.2217805 -0.03639267 -4.7450640 #> X1772062115_E07 -0.8712500 2.7364612 -1.7183691 2.32595033 -3.6333684 #> X1772062109_F01 -1.3272874 1.4356070 -1.0304738 -4.12213852 -4.1252150 #> X1772060226_G05 0.3907491 2.1885820 2.6767877 3.15781103 3.0806766 #> X1772066108_D06 -1.5260866 2.7750273 -0.4384854 2.30825483 0.4356472 #> X1772060224_F07 3.5057101 4.6181601 -2.5965841 0.21805453 -0.2401297 #> X1772062111_F12 1.6046927 2.3747520 0.8362208 0.96854206 -0.4010502 #> X1772063078_G02 -6.5489900 -3.4986779 -0.2621758 -0.41855624 -0.4206648 #> X1772060240_H11 -0.1549005 -2.1274184 -0.5977821 2.88479716 0.5462797 #> X1772067094_C07 1.4112109 0.9021146 1.6095440 -0.99541429 -5.0080497 #> X1772058177_A09 0.8018269 -0.6173596 -1.3570264 -1.58807134 -0.6689549 #> X1772058171_C05 2.2476452 0.7942648 -0.5890266 0.13507711 2.1285625 #> X1772062128_B03 -1.8000638 -1.8281749 0.4248500 0.12789434 0.2856275 #> X1772062118_F04 -1.9157044 4.4401280 6.7268709 -1.04098039 0.3135343 #> X1772062109_E05 2.5019642 -3.2533321 -0.2822758 -2.59738659 0.2083194 #> X1772062128_D02 -0.1884536 -2.2012779 -1.0630142 -0.28033905 0.4069944 #> X1772062109_E12 -1.0375102 0.7080618 2.9863333 1.46002629 -0.2546347 #> X1772062113_E05 4.8313831 -2.2880093 -2.2733269 -2.06696504 1.2045394 #> X1772062128_F05 -1.4619147 1.7619830 0.7601045 -1.01977746 0.8212416 #> X1772062118_D09 -6.3042748 -1.7618979 -4.0076341 3.51991140 0.3576293 #> PC26 PC27 PC28 PC29 PC30 #> X1772063061_G11 0.4393012 0.49066505 -0.9829035 0.2836094 -9.155003e-15 #> X1772067064_C10 -0.8062131 5.25537931 1.1750713 1.0075081 6.215081e-15 #> X1772062113_D09 4.1495959 -2.95029940 4.3919477 2.9514834 -1.119330e-15 #> X1772062111_A12 -2.3263775 0.45981588 1.2528561 0.2735148 1.382575e-15 #> X1772071040_C12 2.9142469 1.43400775 -2.3166794 -1.2525772 7.546047e-15 #> X1772062111_D09 3.0754907 5.59545957 0.7259821 0.5594680 -1.243797e-15 #> X1772071036_G02 2.0455621 -2.67895215 1.4827590 -0.6645307 4.809087e-15 #> X1772071040_D04 -2.1667029 -3.61528611 -2.3513907 -0.8135040 7.243772e-15 #> X1772058177_E12 -0.1039125 -0.84534119 1.8394494 -2.9479911 3.733559e-15 #> X1772066070_G10 0.7574933 -1.65856339 0.7214080 4.5353927 5.015953e-15 #> X1772063074_G10 0.6855627 1.96708841 -2.0012284 -3.0029294 6.374241e-15 #> X1772062115_E07 -2.0707878 -4.37553663 4.2483944 -1.2991642 -1.589007e-15 #> X1772062109_F01 -5.0415991 0.49800107 -4.0551483 4.9262426 4.567093e-15 #> X1772060226_G05 -2.8276955 0.61698889 -1.7035386 1.6909907 -2.332336e-15 #> X1772066108_D06 1.0164694 -0.30406815 -2.2313298 -5.5207653 4.375406e-15 #> X1772060224_F07 -0.1848182 -0.46201188 -1.2313767 -1.8030834 -2.570860e-15 #> X1772062111_F12 2.0001397 -0.76439569 0.8233071 -0.2714401 -7.684825e-16 #> X1772063078_G02 -3.8670764 1.80128883 4.5210094 -0.1818308 6.674349e-16 #> X1772060240_H11 -2.0732482 -0.71925844 -1.1691007 -1.3834397 -8.734333e-16 #> X1772067094_C07 -1.0831410 1.66409517 0.4388037 -0.5433513 -4.128642e-15 #> X1772058177_A09 -1.7670346 -0.89598511 -1.1613516 -0.6051927 -2.072995e-15 #> X1772058171_C05 -0.4055932 0.04484313 1.6260399 0.3516806 -5.442695e-15 #> X1772062128_B03 -0.3535569 -0.07700789 1.0840908 0.4276731 1.255940e-15 #> X1772062118_F04 3.0199296 2.87898511 -0.2517189 1.9514845 -1.422040e-15 #> X1772062109_E05 3.7760216 0.88181574 0.5238567 -0.6462263 -4.942227e-15 #> X1772062128_D02 -0.5191074 -0.20382220 -0.3672539 -0.3945143 -8.239937e-16 #> X1772062109_E12 -2.5630172 -0.52779700 -0.2294288 -0.7521446 -8.202640e-15 #> X1772062113_E05 -0.2032850 0.20715510 -0.8855517 -0.6481144 -5.298713e-15 #> X1772062128_F05 0.1044771 0.26173523 0.7236849 1.2868254 -3.816392e-15 #> X1772062118_D09 4.3788764 -3.97899902 -4.6406595 2.4849262 1.040834e-15