R/preprocessing_filtering_reduction.R
preprocess_TPM.RdPreprocess scExp - Transcripts per Million (TPM)
preprocess_TPM(scExp)
| scExp | A SingleCellExperiment Object |
|---|
A SingleCellExperiment object.
#>#> 6 x 300 sparse Matrix of class "dgCMatrix"#>#> #> chr1_1_5147117 . 190.6705 61.44618 . . #> chr1_5147118_10294233 . . . 27552.81 81.08516 #> chr1_10294234_15441350 122.6678 572.0116 . . . #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 . . 27773.67293 . . #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 31177.24153 . . . . . #> chr1_5147118_10294233 87.33123 . . . 72.34683 . #> chr1_10294234_15441350 87.33121 . . 7066.69774 5498.35834 . #> chr1_15441351_20588466 25850.04282 11230.31 . . 72.34683 . #> chr1_20588467_25735583 87.33121 . . . . . #> chr1_25735584_30882699 . . 9765.98 82.17092 . . #> #> chr1_1_5147117 10251.16381 . . 100.876 . . #> chr1_5147118_10294233 . 85.69903 . . . . #> chr1_10294234_15441350 150.01703 . 89.14825 . . . #> chr1_15441351_20588466 . . 89.14826 . . 96.79707 #> chr1_20588467_25735583 . 85.69902 . . 215.4496 96.79705 #> chr1_25735584_30882699 50.00569 . . . . 96.79707 #> #> chr1_1_5147117 . 73.9368 110.56664 . . #> chr1_5147118_10294233 23539.63751 23733.7189 . 170.15859 8063.42219 #> chr1_10294234_15441350 . . 55.28332 85.07928 . #> chr1_15441351_20588466 51.62201 . 110.56666 . 68.91814 #> chr1_20588467_25735583 . 73.9368 55.28332 . 68.91812 #> chr1_25735584_30882699 51.62201 . . 85.07929 206.75442 #> #> chr1_1_5147117 82.24453 61.7466 . . 12148.8262 #> chr1_5147118_10294233 . . . . 103.8361 #> chr1_10294234_15441350 . . . 207.69143 25128.3413 #> chr1_15441351_20588466 . . 178.6229 . . #> chr1_20588467_25735583 . . . 69.23048 . #> chr1_25735584_30882699 . 123.4932 . . 207.6723 #> #> chr1_1_5147117 . . 74.6285 59.59547 . . #> chr1_5147118_10294233 . . 149.2570 . . 26587.409 #> chr1_10294234_15441350 82.46406 . . 59.59547 . 133.605 #> chr1_15441351_20588466 164.92816 . . 178.78644 83.38173 . #> chr1_20588467_25735583 82.46406 . . 3158.55976 166.76342 . #> chr1_25735584_30882699 . . . . 13257.69436 . #> #> chr1_1_5147117 . . 162.76724 . . #> chr1_5147118_10294233 . 84.3561 . . 76.60337 #> chr1_10294234_15441350 12507.0852 253.0682 . 150.05192 . #> chr1_15441351_20588466 56.8504 . . . . #> chr1_20588467_25735583 . 8098.1838 . 75.02596 . #> chr1_25735584_30882699 . 84.3561 81.38364 . 26198.35205 #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 28094.81355 . 100.4375 17251.4327 7165.15802 #> chr1_10294234_15441350 . . . . 6125.93544 #> chr1_15441351_20588466 . 66.38206 . . 109.39173 #> chr1_20588467_25735583 . . 200.8750 299.1577 54.69585 #> chr1_25735584_30882699 78.47713 . . 199.4385 54.69586 #> #> chr1_1_5147117 . . . . . . #> chr1_5147118_10294233 . . 66.59212 8472.327 . 61.39789 #> chr1_10294234_15441350 . . . . . . #> chr1_15441351_20588466 . . . 25634.220 97.29169 . #> chr1_20588467_25735583 . 188.0292 . . 97.29167 . #> chr1_25735584_30882699 22251.45 . . . 681.04182 . #> #> chr1_1_5147117 . . . . 62.28123 . #> chr1_5147118_10294233 . . . . . . #> chr1_10294234_15441350 . . . . 7037.77865 281.9912 #> chr1_15441351_20588466 32594.57 . . . . . #> chr1_20588467_25735583 . 9982.381 . 84.29719 . . #> chr1_25735584_30882699 . . . 84.29721 . . #> #> chr1_1_5147117 28187.7174 . 179.7681 82.05469 96.73689 #> chr1_5147118_10294233 . 379.15225 . . 96.73691 #> chr1_10294234_15441350 . 63.19203 . . 17267.53510 #> chr1_15441351_20588466 . . 179.7681 82.05471 48.36846 #> chr1_20588467_25735583 110.9753 63.19203 . . . #> chr1_25735584_30882699 . . . 82.05471 8803.05882 #> #> chr1_1_5147117 . . . 75.55301 230.2145 #> chr1_5147118_10294233 . 8376.781 13886.53 . . #> chr1_10294234_15441350 . . . . 115.1073 #> chr1_15441351_20588466 11169.885 . . 226.65906 . #> chr1_20588467_25735583 . . . . 115.1073 #> chr1_25735584_30882699 4434.276 . . 22741.45916 . #> #> chr1_1_5147117 . 198.41700 111.3067 . 159.90176 #> chr1_5147118_10294233 . 10218.47756 . 61.79902 . #> chr1_10294234_15441350 64.90157 . . . . #> chr1_15441351_20588466 64.90158 99.20852 . . . #> chr1_20588467_25735583 129.80313 99.20850 . 123.59801 53.30059 #> chr1_25735584_30882699 129.80316 297.62556 . . 106.60119 #> #> chr1_1_5147117 . 70.91023 . . 8124.73172 #> chr1_5147118_10294233 149.28307 . . . . #> chr1_10294234_15441350 74.64152 . . 445.10131 119.48135 #> chr1_15441351_20588466 74.64154 . 64.43447 . . #> chr1_20588467_25735583 . . . 74.18355 59.74067 #> chr1_25735584_30882699 74.64154 70.91024 . . 119.48137 #> #> chr1_1_5147117 . . 130.93337 . . #> chr1_5147118_10294233 122.2921 89.57418 11587.60535 17177.43060 . #> chr1_10294234_15441350 . 179.14832 65.46668 . . #> chr1_15441351_20588466 24764.1414 627.01923 . 81.79729 2645.125 #> chr1_20588467_25735583 . . 23044.27282 81.79727 5433.229 #> chr1_25735584_30882699 . 12450.81045 . . . #> #> chr1_1_5147117 . 79.44324 . . 163.96127 . #> chr1_5147118_10294233 81.23103 . 132.37222 . 81.98065 . #> chr1_10294234_15441350 . 79.44324 . . 245.94191 124.70972 #> chr1_15441351_20588466 . . 66.18611 . . 62.35487 #> chr1_20588467_25735583 19008.05695 . 132.37219 . 81.98064 . #> chr1_25735584_30882699 81.23103 79.44326 . . 81.98065 2743.61428 #> #> chr1_1_5147117 . . 102.84120 . . #> chr1_5147118_10294233 . 49.15536 . . . #> chr1_10294234_15441350 . 98.31071 . . 8523.779 #> chr1_15441351_20588466 . . 51.42061 . 20684.373 #> chr1_20588467_25735583 . 49.15535 51.42060 . . #> chr1_25735584_30882699 148.1033 8602.18848 . 197.0555 . #> #> chr1_1_5147117 . . . 101.9499 . . #> chr1_5147118_10294233 86.06076 . . . . 181.1343 #> chr1_10294234_15441350 . 47.65268 . . . . #> chr1_15441351_20588466 . . 69.23624 . . . #> chr1_20588467_25735583 86.06074 . . 12335.9340 77.55783 . #> chr1_25735584_30882699 . 47.65269 69.23624 203.8998 . . #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 . . . 185.41853 69.34928 #> chr1_10294234_15441350 8281.5914 . 22888.4137 92.70925 138.69854 #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 106.1742 278.2928 . . . #> chr1_25735584_30882699 . . 128.2264 13442.84370 14910.09600 #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 117.3544 . . 78.28084 20238.21 #> chr1_10294234_15441350 . 229.4355 45.44235 78.28082 . #> chr1_15441351_20588466 . . 5543.96740 . . #> chr1_20588467_25735583 . 76.4785 45.44235 39923.21884 . #> chr1_25735584_30882699 . 17513.5803 . 234.84251 . #> #> chr1_1_5147117 126.9751 . . . . . #> chr1_5147118_10294233 . . 16077.01995 . 86.61724 . #> chr1_10294234_15441350 . 17172.4508 130.70745 . 346.46888 . #> chr1_15441351_20588466 . . 65.35374 57.37514 . . #> chr1_20588467_25735583 . . 130.70745 . . . #> chr1_25735584_30882699 . 66.0479 . . . . #> #> chr1_1_5147117 . 163.05066 . . . . #> chr1_5147118_10294233 138.97832 . 76.74178 . . . #> chr1_10294234_15441350 . 652.20263 . 12650.09 . 52.68623 #> chr1_15441351_20588466 69.48916 163.05069 . . . 52.68624 #> chr1_20588467_25735583 . 81.52533 . 104.98 . 52.68623 #> chr1_25735584_30882699 . . 12201.94364 . . . #> #> chr1_1_5147117 . . 97.8981 . . #> chr1_5147118_10294233 76.58981 . . . 146.1024 #> chr1_10294234_15441350 . . 195.7962 60.02504 . #> chr1_15441351_20588466 . . . 60.02505 17897.5466 #> chr1_20588467_25735583 7276.03099 . . 120.05008 . #> chr1_25735584_30882699 . 482.5037 . . . #> #> chr1_1_5147117 . . . . 48.44668 #> chr1_5147118_10294233 . . 73.91997 113.02236 . #> chr1_10294234_15441350 8869.008 9448.46383 . . 10561.37627 #> chr1_15441351_20588466 . 73.81614 . 56.51118 . #> chr1_20588467_25735583 . . . . . #> chr1_25735584_30882699 . 73.81614 . . 96.89338 #> #> chr1_1_5147117 65.98475 5841.56507 30515.59 . . #> chr1_5147118_10294233 . 70.38032 . 70.04693 139.7008 #> chr1_10294234_15441350 . . . 140.09384 . #> chr1_15441351_20588466 . 281.52126 . . 139.7008 #> chr1_20588467_25735583 23490.57033 . . . . #> chr1_25735584_30882699 . . . . 18230.9596 #> #> chr1_1_5147117 . . . . 72.18098 #> chr1_5147118_10294233 14332.51513 . . . 11476.77730 #> chr1_10294234_15441350 67.60619 . 93.54975 . 72.18098 #> chr1_15441351_20588466 . . . . 12270.76818 #> chr1_20588467_25735583 . 85.09659 . 72.90046 72.18098 #> chr1_25735584_30882699 . 85.09660 93.54977 72.90047 . #> #> chr1_1_5147117 . . 215.58408 . . #> chr1_5147118_10294233 . 80.06978 . . . #> chr1_10294234_15441350 . . . . 78.92719 #> chr1_15441351_20588466 67.37652 . . . . #> chr1_20588467_25735583 13071.04248 80.06976 . 83.49706 . #> chr1_25735584_30882699 . . 71.86137 83.49708 157.85441 #> #> chr1_1_5147117 143.54758 64.02888 . . . #> chr1_5147118_10294233 95.69840 . . . . #> chr1_10294234_15441350 47.84919 . . 69.59823 28717.26427 #> chr1_15441351_20588466 . . 71.89370 . . #> chr1_20588467_25735583 . 192.08663 71.89369 . 90.02277 #> chr1_25735584_30882699 . . 143.78740 . . #> #> chr1_1_5147117 . 62.53198 . 103.9706 . #> chr1_5147118_10294233 81.98265 . 165.5542 103.9707 . #> chr1_10294234_15441350 . . . 13360.2278 . #> chr1_15441351_20588466 . 14507.42311 165.5542 . 90.19766 #> chr1_20588467_25735583 . . . . . #> chr1_25735584_30882699 22217.29719 . 11754.3500 207.9413 . #> #> chr1_1_5147117 24275.19171 . 16869.72679 78.64235 502.31102 #> chr1_5147118_10294233 87.00787 90.99264 . . 19087.82262 #> chr1_10294234_15441350 174.01571 . . . 83.71850 #> chr1_15441351_20588466 . . 60.90155 . 83.71852 #> chr1_20588467_25735583 . . . . 251.15551 #> chr1_25735584_30882699 261.02362 . . . . #> #> chr1_1_5147117 . . 14963.190 46.14592 . #> chr1_5147118_10294233 77.46947 79.12598 . 46.14593 . #> chr1_10294234_15441350 77.46945 79.12597 128.993 . . #> chr1_15441351_20588466 7282.13014 79.12598 . 6368.13884 . #> chr1_20588467_25735583 77.46945 21443.13717 . 46.14592 30588.94 #> chr1_25735584_30882699 77.46947 . . 46.14593 . #> #> chr1_1_5147117 7793.93265 . . . . #> chr1_5147118_10294233 . 492.65231 . . 18039.97005 #> chr1_10294234_15441350 84.71666 . . 20388.52245 . #> chr1_15441351_20588466 . 82.10872 95.41575 14676.56570 . #> chr1_20588467_25735583 254.14998 . . 79.33277 82.75214 #> chr1_25735584_30882699 20332.00216 164.21744 . . . #> #> chr1_1_5147117 . . . . . . #> chr1_5147118_10294233 58.01067 . 70.36737 407.40566 76.4839 . #> chr1_10294234_15441350 . . 70.36736 . . . #> chr1_15441351_20588466 . 247.4521 . . . 26685.657 #> chr1_20588467_25735583 58.01066 82.4840 . 67.90093 . 7157.667 #> chr1_25735584_30882699 . . . . . . #> #> chr1_1_5147117 . 125.32406 125.1415 . . #> chr1_5147118_10294233 . 1817.19928 . . . #> chr1_10294234_15441350 75.48772 62.66203 . 6663.42936 8842.0697 #> chr1_15441351_20588466 150.97547 . . . 171.6907 #> chr1_20588467_25735583 . . . 60.57663 . #> chr1_25735584_30882699 21815.95564 62.66204 . 2907.67883 . #> #> chr1_1_5147117 . 29487.21 . 84.53478 263.89515 #> chr1_5147118_10294233 153.63533 . . . . #> chr1_10294234_15441350 153.63530 . . . . #> chr1_15441351_20588466 76.81767 . 108.6774 169.06958 87.96507 #> chr1_20588467_25735583 76.81765 . . 37279.83598 . #> chr1_25735584_30882699 153.63533 . . . 87.96507 #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 . . . 125.6566 56.38545 #> chr1_10294234_15441350 . 9330.293 . 27455.9703 9698.29508 #> chr1_15441351_20588466 78.07888 . . . . #> chr1_20588467_25735583 156.15773 . . 125.6566 . #> chr1_25735584_30882699 78.07888 . 14371.29 . . #> #> chr1_1_5147117 . . 84.99406 . . #> chr1_5147118_10294233 134.4376 . 169.98815 70.94727 . #> chr1_10294234_15441350 . . . . 83.5957 #> chr1_15441351_20588466 . . 10964.23552 141.89455 . #> chr1_20588467_25735583 . 6134.3007 84.99406 . 83.5957 #> chr1_25735584_30882699 . 134.8198 1359.90518 . . #> #> chr1_1_5147117 . . . . 67.78433 #> chr1_5147118_10294233 2507.95166 81.36821 . . . #> chr1_10294234_15441350 17457.30716 81.36819 170.5565 . 15048.12053 #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 49.17551 5614.40531 20381.5050 . 10371.00198 #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 . 135.95880 . . 6378.5073 #> chr1_5147118_10294233 . 67.97941 75.69993 23189.18996 . #> chr1_10294234_15441350 . . 75.69991 . 155.5733 #> chr1_15441351_20588466 . 135.95882 151.39985 . 9412.1895 #> chr1_20588467_25735583 58.85261 67.97940 . 13897.62827 4744.9872 #> chr1_25735584_30882699 17891.19768 . 75.69993 79.41503 . #> #> chr1_1_5147117 18254.89845 . 22030.3406 . 81.80973 #> chr1_5147118_10294233 . 83.27571 . . . #> chr1_10294234_15441350 . . . . 81.80973 #> chr1_15441351_20588466 . . 172.1121 . 163.61950 #> chr1_20588467_25735583 71.58784 . . 103.7198 . #> chr1_25735584_30882699 143.17570 . . . 163.61950 #> #> chr1_1_5147117 . . . . 60.28251 . #> chr1_5147118_10294233 . . . . 7294.18515 . #> chr1_10294234_15441350 . . 21356.6573 . 120.56502 115.33175 #> chr1_15441351_20588466 66.18227 69.03487 . . 301.41261 57.66589 #> chr1_20588467_25735583 397.09357 . . . . . #> chr1_25735584_30882699 66.18227 69.03487 163.0279 . 60.28252 . #> #> chr1_1_5147117 . . . 52.19818 158.50148 #> chr1_5147118_10294233 . . 82.23957 104.39638 . #> chr1_10294234_15441350 . . 24013.94845 . 52.83383 #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 239.7472 . . 104.39636 . #> chr1_25735584_30882699 . 141.8032 82.23957 . . #> #> chr1_1_5147117 . 201.2512 63.36344 5043.3466 . #> chr1_5147118_10294233 . . . . 19923.81 #> chr1_10294234_15441350 12146.62289 . . . . #> chr1_15441351_20588466 8833.90928 . . . . #> chr1_20588467_25735583 92.01987 . . 148.3337 . #> chr1_25735584_30882699 184.03978 . . . . #> #> chr1_1_5147117 . 199.54867 . . . #> chr1_5147118_10294233 . . . . 95.47465 #> chr1_10294234_15441350 118.9304 . 89.25643 . 20336.09581 #> chr1_15441351_20588466 1902.8868 . . 71.98532 . #> chr1_20588467_25735583 . 66.51622 . 143.97060 . #> chr1_25735584_30882699 . 133.03247 267.76934 . . #> #> chr1_1_5147117 170.00187 . 73.81151 . 8886.35681 #> chr1_5147118_10294233 170.00191 . . . . #> chr1_10294234_15441350 . . . . . #> chr1_15441351_20588466 85.00095 8985.4964 . . 71.09087 #> chr1_20588467_25735583 85.00094 . . 83.87274 . #> chr1_25735584_30882699 . 88.0931 . . . #> #> chr1_1_5147117 152.5145 . . . 53.32389 #> chr1_5147118_10294233 . 16327.35 62.38864 . . #> chr1_10294234_15441350 . . . 74.03843 . #> chr1_15441351_20588466 152.5145 . 35311.96787 . . #> chr1_20588467_25735583 . 27058.94 27575.77167 15029.80187 53.32389 #> chr1_25735584_30882699 . . 124.77727 148.07689 12744.41153 #> #> chr1_1_5147117 . . . 12879.19226 . 112.09505 #> chr1_5147118_10294233 . . 142.36356 . . . #> chr1_10294234_15441350 1520.77093 . 6833.44971 8438.09148 . . #> chr1_15441351_20588466 . . 71.18178 63.44431 . . #> chr1_20588467_25735583 . . 18436.07788 . . 56.04752 #> chr1_25735584_30882699 69.12597 . 71.18178 . . 336.28521 #> #> chr1_1_5147117 176.54293 102.2551 6032.932 179.40459 175.15206 #> chr1_5147118_10294233 . 102.2551 . 179.40462 . #> chr1_10294234_15441350 15535.77803 . 59.732 179.40459 . #> chr1_15441351_20588466 . . . . 87.57604 #> chr1_20588467_25735583 88.27147 102.2551 . 89.70229 . #> chr1_25735584_30882699 . . . . 87.57604 #> #> chr1_1_5147117 139.9618 3280.8524 . 68.34277 125.35859 #> chr1_5147118_10294233 18055.0700 88.6717 . . 62.67931 #> chr1_10294234_15441350 . . 12519.09 . . #> chr1_15441351_20588466 . . . 68.34278 . #> chr1_20588467_25735583 . . . . 62.67930 #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 91.61765 25062.58 . 71.15544 . . #> chr1_5147118_10294233 183.23533 . 178.69258 71.15546 . . #> chr1_10294234_15441350 . . . . . 19714.55 #> chr1_15441351_20588466 . . 178.69258 142.31092 . . #> chr1_20588467_25735583 366.47059 15784.09 . 12523.35828 . . #> chr1_25735584_30882699 . . 89.34629 . . . #> #> chr1_1_5147117 . 6172.52329 . 90.01460 13466.5369 #> chr1_5147118_10294233 . . . 90.01461 13862.6142 #> chr1_10294234_15441350 . 27275.87993 272.13747 . 132.0249 #> chr1_15441351_20588466 . 83.41249 35196.45262 . . #> chr1_20588467_25735583 387.8146 . 90.71249 13592.20401 . #> chr1_25735584_30882699 . . . . 23302.3943 #> #> chr1_1_5147117 9005.21133 . . . . . #> chr1_5147118_10294233 . . 173.5189 . . 20251.35930 #> chr1_10294234_15441350 68.74207 . . 69.9908 . . #> chr1_15441351_20588466 . . . . 181.1578 69.11727 #> chr1_20588467_25735583 . . . . . . #> chr1_25735584_30882699 412.45251 . . . 6883.9980 138.23453 #> #> chr1_1_5147117 . 221.17431 . 19106.0655 65.26253 #> chr1_5147118_10294233 . . 289.77880 226.7783 . #> chr1_10294234_15441350 137.2605 73.72477 . . 16250.36932 #> chr1_15441351_20588466 15579.0680 19758.24193 . 113.3891 130.52508 #> chr1_20588467_25735583 . . 96.59292 . 65.26253 #> chr1_25735584_30882699 . 73.72478 193.18587 6349.7915 . #> #> chr1_1_5147117 17135.05287 18407.4822 75.41490 . 281.7774 #> chr1_5147118_10294233 . 8410.9111 75.41492 . 187.8517 #> chr1_10294234_15441350 12651.11380 . . 72.38967 . #> chr1_15441351_20588466 . . . 72.38969 31746.9292 #> chr1_20588467_25735583 . 137.8838 . . 20287.9745 #> chr1_25735584_30882699 80.07036 . 150.82983 . . #> #> chr1_1_5147117 3049.8952 53.17553 . . . . #> chr1_5147118_10294233 . . . 9738.21034 509.9355 10721.70301 #> chr1_10294234_15441350 108.9248 . . 5026.17210 127.4838 63.06883 #> chr1_15441351_20588466 . . . 78.53395 . 63.06884 #> chr1_20588467_25735583 . . . 785.33939 . . #> chr1_25735584_30882699 . . . . 127.4839 . #> #> chr1_1_5147117 . . . . . 107.4821 #> chr1_5147118_10294233 12980.77 . . . 17823.46 107.4822 #> chr1_10294234_15441350 . . 86.89116 . . . #> chr1_15441351_20588466 . . 86.89118 . . . #> chr1_20588467_25735583 . . . . . 107.4821 #> chr1_25735584_30882699 . 66.09174 19463.62324 . . . #> #> chr1_1_5147117 . 111.1219 156.0545 . #> chr1_5147118_10294233 . 111.1220 . . #> chr1_10294234_15441350 . . . 110.8019 #> chr1_15441351_20588466 . . . . #> chr1_20588467_25735583 . . . 1440.4249 #> chr1_25735584_30882699 208.2171 . . .