R/preprocessing_filtering_reduction.R
preprocess_CPM.RdPreprocess scExp - Counts Per Million (CPM)
preprocess_CPM(scExp)
| scExp | A SingleCellExperiment Object |
|---|
A SingleCellExperiment object.
#>#> 6 x 300 sparse Matrix of class "dgCMatrix"#>#> #> chr1_1_5147117 66.12882 42641.7057 . . . . #> chr1_5147118_10294233 . 65.0026 . . 145.16949 . #> chr1_10294234_15441350 21425.73734 . 114.1422 . 72.58474 92.84189 #> chr1_15441351_20588466 66.12882 . . . 5951.94890 . #> chr1_20588467_25735583 . 65.0026 114.1422 . . . #> chr1_25735584_30882699 8398.36001 . 798.9955 . 72.58474 . #> #> chr1_1_5147117 . 11517.9833 . 90.23642 . . #> chr1_5147118_10294233 92.36169 . 95.50186 . . 99.92006 #> chr1_10294234_15441350 . . 95.50186 . . . #> chr1_15441351_20588466 18472.33767 217.3204 21201.41343 90.23642 . . #> chr1_20588467_25735583 . 108.6602 . 90.23642 . . #> chr1_25735584_30882699 . 108.6602 95.50186 . . 99.92006 #> #> chr1_1_5147117 . 31704.5098 . . 99.36407 #> chr1_5147118_10294233 168.5204 . . . . #> chr1_10294234_15441350 . 209.2707 . 146.97237 . #> chr1_15441351_20588466 . 26577.3778 . 73.48618 . #> chr1_20588467_25735583 . . 70.04273 . . #> chr1_25735584_30882699 . . 140.08545 . . #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 . . . 28186.27451 . #> chr1_10294234_15441350 12895.38 76.81081 . . 13100.74760 #> chr1_15441351_20588466 . . 154.55951 22846.63866 71.19972 #> chr1_20588467_25735583 13300.89 76.81081 77.27975 87.53501 142.39943 #> chr1_25735584_30882699 . 460.86489 . 87.53501 71.19972 #> #> chr1_1_5147117 14680.02813 19106.3638 . . . #> chr1_5147118_10294233 87.90436 . 167.79931 86.44537 117.9384 #> chr1_10294234_15441350 . 75.2219 . . 26536.1481 #> chr1_15441351_20588466 . . . 86.44537 . #> chr1_20588467_25735583 87.90436 225.6657 251.69897 86.44537 117.9384 #> chr1_25735584_30882699 87.90436 . 83.89966 86.44537 117.9384 #> #> chr1_1_5147117 95.63887 . 89.32559 . . #> chr1_5147118_10294233 . . 178.65118 . . #> chr1_10294234_15441350 . 320.7698 . . . #> chr1_15441351_20588466 . . 89.32559 90.5469 21781.64 #> chr1_20588467_25735583 191.27774 17080.9944 . . 19758.58 #> chr1_25735584_30882699 95.63887 . . . . #> #> chr1_1_5147117 . . . 23448.04318 . #> chr1_5147118_10294233 23571.0077 . . . . #> chr1_10294234_15441350 . . 173.19016 84.34548 . #> chr1_15441351_20588466 . . 259.78524 84.34548 . #> chr1_20588467_25735583 . 212.3142 86.59508 21423.75169 . #> chr1_25735584_30882699 147.3188 . 86.59508 . 81.97393 #> #> chr1_1_5147117 . . . 71.46941 204.165 127.7466 #> chr1_5147118_10294233 81.7929 . 91.42439 9148.08462 . 127.7466 #> chr1_10294234_15441350 3271.7160 . . . 12964.475 255.4931 #> chr1_15441351_20588466 . . . 71.46941 . . #> chr1_20588467_25735583 . . 91.42439 . . . #> chr1_25735584_30882699 . . 91.42439 71.46941 . 127.7466 #> #> chr1_1_5147117 14008.62069 . . 23229.85699 . #> chr1_5147118_10294233 . . . 69.75933 . #> chr1_10294234_15441350 . 98.84353 149.1647 . . #> chr1_15441351_20588466 82.89125 10180.88366 . 69.75933 . #> chr1_20588467_25735583 . 98.84353 149.1647 . . #> chr1_25735584_30882699 165.78249 12553.12840 . . . #> #> chr1_1_5147117 . . 191.00372 . . #> chr1_5147118_10294233 . . . . . #> chr1_10294234_15441350 88.8573 8931.79358 95.50186 88.07469 . #> chr1_15441351_20588466 . . . . 24466.80824 #> chr1_20588467_25735583 . . . . 92.32758 #> chr1_25735584_30882699 28789.7636 90.22014 . 176.14937 276.98273 #> #> chr1_1_5147117 82.80202 27151.56671 . . 75.73463 #> chr1_5147118_10294233 165.60404 70.89182 98.09692 . 75.73463 #> chr1_10294234_15441350 16643.20609 70.89182 . 190.1141 . #> chr1_15441351_20588466 165.60404 . . . . #> chr1_20588467_25735583 . . 196.19384 190.1141 . #> chr1_25735584_30882699 82.80202 . . 15969.5817 . #> #> chr1_1_5147117 . 70.50694 . 574.38254 153.5155 #> chr1_5147118_10294233 . . . 8711.46850 . #> chr1_10294234_15441350 85.91065 70.50694 79.96162 . . #> chr1_15441351_20588466 85.91065 70.50694 . . 153.5155 #> chr1_20588467_25735583 . . 79.96162 95.73042 . #> chr1_25735584_30882699 . 141.01389 . 1148.76508 . #> #> chr1_1_5147117 71.87006 . . . . #> chr1_5147118_10294233 . 97.18173 . 12850.36654 . #> chr1_10294234_15441350 . 583.09038 31992.69 . . #> chr1_15441351_20588466 12649.13037 . . 86.24407 190.2769 #> chr1_20588467_25735583 6108.95501 97.18173 . . . #> chr1_25735584_30882699 503.09041 8260.44704 14791.42 86.24407 . #> #> chr1_1_5147117 79.14523 . . 229.5421 . #> chr1_5147118_10294233 79.14523 . . 114.7710 79.47862 #> chr1_10294234_15441350 79.14523 91.86955 . 114.7710 . #> chr1_15441351_20588466 . 183.73909 . . . #> chr1_20588467_25735583 . 551.21727 16854.85191 . . #> chr1_25735584_30882699 38543.72774 . 81.81967 . . #> #> chr1_1_5147117 20243.54301 96.35768 . . 23471.92 #> chr1_5147118_10294233 77.56147 . . . . #> chr1_10294234_15441350 . . 87.10801 . . #> chr1_15441351_20588466 . 96.35768 87.10801 . . #> chr1_20588467_25735583 155.12293 . . 345.2741 . #> chr1_25735584_30882699 77.56147 . 87.10801 . . #> #> chr1_1_5147117 91.14939 . . . 72.55315 #> chr1_5147118_10294233 182.29879 . . . . #> chr1_10294234_15441350 . 246.6294 . 82.81573 . #> chr1_15441351_20588466 . 82.2098 234.1007 . 290.21258 #> chr1_20588467_25735583 . 164.4196 . 82.81573 19154.03033 #> chr1_25735584_30882699 . . . 7619.04762 145.10629 #> #> chr1_1_5147117 101.6054 29210.08104 77.79074 . 1595.914 #> chr1_5147118_10294233 609.6322 89.05513 77.79074 . . #> chr1_10294234_15441350 . . . 191.9017 . #> chr1_15441351_20588466 . 267.16538 155.58149 . . #> chr1_20588467_25735583 . . 77.79074 . . #> chr1_25735584_30882699 101.6054 . 77.79074 191.9017 . #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 . . . . 80.5153 #> chr1_10294234_15441350 . 6128.621 . . 322.0612 #> chr1_15441351_20588466 . 159.185 . . 11433.1723 #> chr1_20588467_25735583 86.38563 19500.159 88.90469 . . #> chr1_25735584_30882699 . . 16269.55903 25390.47 . #> #> chr1_1_5147117 101.4507 . 89.83919 8697.5196 . . #> chr1_5147118_10294233 . . . 107.3768 7302.654 77.15454 #> chr1_10294234_15441350 608.7045 . 179.67838 . . . #> chr1_15441351_20588466 101.4507 . . 107.3768 . 77.15454 #> chr1_20588467_25735583 101.4507 . 179.67838 . . . #> chr1_25735584_30882699 . . . . . . #> #> chr1_1_5147117 16159.00461 . . 152.26494 77.36944 #> chr1_5147118_10294233 . . . . . #> chr1_10294234_15441350 242.38507 10584.38 . 228.39741 . #> chr1_15441351_20588466 242.38507 . 95.59316 76.13247 . #> chr1_20588467_25735583 80.79502 14907.57 12140.33075 . . #> chr1_25735584_30882699 . . . 152.26494 77.36944 #> #> chr1_1_5147117 13927.1120 70.70636 . . 168.86187 #> chr1_5147118_10294233 166.7918 . 510.72523 82.28421 . #> chr1_10294234_15441350 . . . 20982.47346 84.43094 #> chr1_15441351_20588466 . 141.41271 85.12087 . 23302.93820 #> chr1_20588467_25735583 . . . 82.28421 . #> chr1_25735584_30882699 13843.7161 . 30558.39292 . . #> #> chr1_1_5147117 . . 164.16318 . . #> chr1_5147118_10294233 . . . 77.54944 . #> chr1_10294234_15441350 . 25238.17 82.08159 . 16883.34 #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 . . 164.16318 . 31065.34 #> chr1_25735584_30882699 80.80155 . . 5273.36177 . #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 76.67536 . 85.07018 . 4161.4648 #> chr1_10294234_15441350 76.67536 . . . 104.0366 #> chr1_15441351_20588466 . 97.35202 85.07018 . . #> chr1_20588467_25735583 24612.78945 . . 14872.4 14565.1269 #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 88.9126 . 76.01672 . 161.3684 11377.4888 #> chr1_5147118_10294233 . . . 129.39959 80.6842 203.1694 #> chr1_10294234_15441350 . . . 16045.54865 80.6842 101.5847 #> chr1_15441351_20588466 34053.5254 . 12162.67579 . . 203.1694 #> chr1_20588467_25735583 . . 152.03345 . . . #> chr1_25735584_30882699 88.9126 . . 64.69979 . 13612.3527 #> #> chr1_1_5147117 . 295.8288 63.11139 87.78861 . #> chr1_5147118_10294233 101.7915 98.6096 . . . #> chr1_10294234_15441350 101.7915 11734.5429 . . . #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 101.7915 98.6096 9277.37457 . . #> chr1_25735584_30882699 . . . 175.57721 26197.86 #> #> chr1_1_5147117 6666.049 . 66.17258 30752.21 . #> chr1_5147118_10294233 33700.583 99.71084 66.17258 . . #> chr1_10294234_15441350 . . . . 28102.4914 #> chr1_15441351_20588466 . 99.71084 . . 236.1554 #> chr1_20588467_25735583 . . 397.03547 . . #> chr1_25735584_30882699 . 199.42168 198.51773 . . #> #> chr1_1_5147117 98.74593 . . 103.6699 . . #> chr1_5147118_10294233 296.23778 100.4924 163.6929 . . 234.66834 #> chr1_10294234_15441350 98.74593 . 491.0787 . 93.55412 . #> chr1_15441351_20588466 . . . . 93.55412 78.22278 #> chr1_20588467_25735583 . 200.9848 . . 93.55412 156.44556 #> chr1_25735584_30882699 . 100.4924 . . 93.55412 . #> #> chr1_1_5147117 . . 79.55449 85.99931 125.4705 #> chr1_5147118_10294233 70.24939 84.33125 . . . #> chr1_10294234_15441350 . 84.33125 238.66348 . . #> chr1_15441351_20588466 . . . 171.99862 376.4115 #> chr1_20588467_25735583 . 168.66251 36197.29515 85.99931 . #> chr1_25735584_30882699 70.24939 . 18695.30628 . . #> #> chr1_1_5147117 . 17041.24475 176.6784 . 8144.151 #> chr1_5147118_10294233 81.06355 . . 40201.34685 . #> chr1_10294234_15441350 . . . 68.02258 . #> chr1_15441351_20588466 . 82.32485 . . . #> chr1_20588467_25735583 . . . 68.02258 . #> chr1_25735584_30882699 567.44488 82.32485 . . . #> #> chr1_1_5147117 . 78.1311 . . . #> chr1_5147118_10294233 . 78.1311 . 101.0714 15094.60 #> chr1_10294234_15441350 . . . . 16597.23 #> chr1_15441351_20588466 11160.714 . . 38710.3295 . #> chr1_20588467_25735583 . 468.7866 . . . #> chr1_25735584_30882699 6231.399 . 74.32181 . . #> #> chr1_1_5147117 74.69376 148.54427 . . . #> chr1_5147118_10294233 13071.40723 . . . 90.90083 #> chr1_10294234_15441350 . 74.27213 . 16164.52268 . #> chr1_15441351_20588466 149.38751 . . . 30542.67794 #> chr1_20588467_25735583 74.69376 . . 84.63101 . #> chr1_25735584_30882699 . . 105.9322 84.63101 30179.07463 #> #> chr1_1_5147117 74.54342 . . 125.63603 . #> chr1_5147118_10294233 . 89.02341 . . . #> chr1_10294234_15441350 . 267.07024 91.55832 . 158.1653 #> chr1_15441351_20588466 74.54342 25638.74299 43398.64494 14825.05182 . #> chr1_20588467_25735583 74.54342 13709.60563 91.55832 62.81802 . #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 . 74.67145 90.86779 . . #> chr1_5147118_10294233 . 11126.04540 . . . #> chr1_10294234_15441350 . . 90.86779 11379.8009 . #> chr1_15441351_20588466 85.88114 . . . . #> chr1_20588467_25735583 85.88114 12843.48865 181.73557 101.6054 79.85945 #> chr1_25735584_30882699 85.88114 . . . 79.85945 #> #> chr1_1_5147117 . . . 167.70082 82.39947 #> chr1_5147118_10294233 181.17583 . 81.686 . 11865.52406 #> chr1_10294234_15441350 . 76.4526 29080.216 83.85041 494.39684 #> chr1_15441351_20588466 90.58792 76.4526 . . . #> chr1_20588467_25735583 181.17583 76.4526 81.686 83.85041 . #> chr1_25735584_30882699 181.17583 . . 83.85041 494.39684 #> #> chr1_1_5147117 204.5199 18016.58163 . . . #> chr1_5147118_10294233 204.5199 . . 80.2375 11569.92 #> chr1_10294234_15441350 204.5199 . 403.17162 25756.2385 . #> chr1_15441351_20588466 . 79.71939 . 7702.8003 . #> chr1_20588467_25735583 . . 19822.60449 . . #> chr1_25735584_30882699 . . 67.19527 . . #> #> chr1_1_5147117 83.68201 . . . . . #> chr1_5147118_10294233 . 22199.0076 . 120.8167 . 210.084 #> chr1_10294234_15441350 83.68201 65.2912 . . . 105.042 #> chr1_15441351_20588466 . 65.2912 . . . . #> chr1_20588467_25735583 167.36402 . . . 101.5435 . #> chr1_25735584_30882699 167.36402 65.2912 . 120.8167 . 210.084 #> #> chr1_1_5147117 . 108.3776 . . 4630.5754 . #> chr1_5147118_10294233 75.09199 . . 11662.05 . . #> chr1_10294234_15441350 . 18749.3226 . . . . #> chr1_15441351_20588466 . . . . 68.0967 . #> chr1_20588467_25735583 . . . . . . #> chr1_25735584_30882699 . 216.7552 78.02747 . 68.0967 . #> #> chr1_1_5147117 101.2248 . . . 85.6531 255.4713 #> chr1_5147118_10294233 . 96.35768 . . . . #> chr1_10294234_15441350 101.2248 . . . 171.3062 15328.2807 #> chr1_15441351_20588466 . 96.35768 9121.061 92.0556 . 255.4713 #> chr1_20588467_25735583 101.2248 . . . 85.6531 . #> chr1_25735584_30882699 . . . 2577.5568 . . #> #> chr1_1_5147117 . . . 522.6026 . #> chr1_5147118_10294233 . . . . 9949.83965 #> chr1_10294234_15441350 . 14355.29 15335.88931 . 82.23008 #> chr1_15441351_20588466 84.63101 19225.84 83.34722 . . #> chr1_20588467_25735583 84.63101 . 83.34722 . . #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 83.97011 . . 98.39614 192.7277 . #> chr1_5147118_10294233 167.94021 . 35429.93631 98.39614 . 68.11061 #> chr1_10294234_15441350 . . . . 128.4852 68.11061 #> chr1_15441351_20588466 83.97011 . . . 10856.9960 . #> chr1_20588467_25735583 83.97011 . 79.61783 . . . #> chr1_25735584_30882699 . . 79.61783 . 192.7277 15324.88762 #> #> chr1_1_5147117 21287.83876 . . 451.02608 . #> chr1_5147118_10294233 . . 82.7746 75.17101 91.19095 #> chr1_10294234_15441350 75.48879 109.1703 82.7746 75.17101 . #> chr1_15441351_20588466 . 218.3406 . 75.17101 91.19095 #> chr1_20588467_25735583 . . . 150.34203 . #> chr1_25735584_30882699 75.48879 . . . 16779.13551 #> #> chr1_1_5147117 77.20815 . 232.342 . . #> chr1_5147118_10294233 . . . 63.17119 . #> chr1_10294234_15441350 . . 10223.048 . . #> chr1_15441351_20588466 . . . 24257.73847 16312.81 #> chr1_20588467_25735583 77.20815 86.27383 . 63.17119 . #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 . 83.18084 . . . . #> chr1_5147118_10294233 . . . . 65.53509 220.8806 #> chr1_10294234_15441350 . . 85.6311 . . 147.2537 #> chr1_15441351_20588466 128.3203 83.18084 . 27808.44604 . . #> chr1_20588467_25735583 . 83.18084 85.6311 . 65.53509 . #> chr1_25735584_30882699 . 166.36167 . 69.00359 65.53509 . #> #> chr1_1_5147117 . 79.2142 . 254.30194 78.64108 . #> chr1_5147118_10294233 91.49131 . . 20174.62067 78.64108 . #> chr1_10294234_15441350 91.49131 . . . . 85.17162 #> chr1_15441351_20588466 . 79.2142 155.9697 84.76731 . 85.17162 #> chr1_20588467_25735583 . . . . . 85.17162 #> chr1_25735584_30882699 . 79.2142 . . 157.28216 . #> #> chr1_1_5147117 . . . . 8123.20190 79.44074 #> chr1_5147118_10294233 417.9292 . . 97.07795 84.61669 . #> chr1_10294234_15441350 . . . . . . #> chr1_15441351_20588466 . . . 97.07795 592.31680 79.44074 #> chr1_20588467_25735583 104.4823 234.7418 . 97.07795 28261.97326 79.44074 #> chr1_25735584_30882699 . 156.4945 74.64915 97.07795 . . #> #> chr1_1_5147117 . . 159.7189 . 13469.62170 #> chr1_5147118_10294233 . . . 309.2624 . #> chr1_10294234_15441350 . 71.61272 13096.9494 . . #> chr1_15441351_20588466 . . . . 191.05846 #> chr1_20588467_25735583 93.3184 71.61272 159.7189 . . #> chr1_25735584_30882699 186.6368 5729.01747 . . 95.52923 #> #> chr1_1_5147117 97.86651 155.8482 . . . #> chr1_5147118_10294233 38167.93893 . . . . #> chr1_10294234_15441350 . . 99.75062 . . #> chr1_15441351_20588466 195.73302 77.9241 . . . #> chr1_20588467_25735583 . 2415.6472 . 20108.41 82.78831 #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 9193.1646 711.3219 . . 76.13247 #> chr1_5147118_10294233 648.9293 237.1073 . . . #> chr1_10294234_15441350 108.1549 . . 94.10879 76.13247 #> chr1_15441351_20588466 . 355.6609 . 94.10879 . #> chr1_20588467_25735583 . 48606.9947 225.3267 . 152.26494 #> chr1_25735584_30882699 12113.3463 . . . 21393.22421 #> #> chr1_1_5147117 73.48618 179.72682 77.47734 . 77.67594 #> chr1_5147118_10294233 . . . 162.7737 77.67594 #> chr1_10294234_15441350 73.48618 179.72682 . . 3650.76899 #> chr1_15441351_20588466 . . . . 77.67594 #> chr1_20588467_25735583 . . 77.47734 24904.3705 . #> chr1_25735584_30882699 146.97237 89.86341 77.47734 . . #> #> chr1_1_5147117 102.9866 20270.71209 . 83.22237 . . . #> chr1_5147118_10294233 . . . 166.44474 . . . #> chr1_10294234_15441350 . 65.38939 . 499.33422 242.11121 . . #> chr1_15441351_20588466 205.9732 392.33636 . . . 168.1237 . #> chr1_20588467_25735583 . 261.55758 . . 80.70374 504.3712 . #> chr1_25735584_30882699 . 10723.86059 . . . . . #> #> chr1_1_5147117 . . 94.62528 84.488 . #> chr1_5147118_10294233 91.09957 . . . . #> chr1_10294234_15441350 . 5527.3548 . . . #> chr1_15441351_20588466 . . . 84.488 . #> chr1_20588467_25735583 21590.59852 112.8032 662.37699 . . #> chr1_25735584_30882699 . 225.6063 189.25057 . 142.8673 #> #> chr1_1_5147117 . 89.63786 74.64915 87.58101 . #> chr1_5147118_10294233 . . . . 270.44082 #> chr1_10294234_15441350 74.04117 . . . 90.14694 #> chr1_15441351_20588466 148.08233 . . 18392.01261 . #> chr1_20588467_25735583 74.04117 . . . . #> chr1_25735584_30882699 148.08233 . . . . #> #> chr1_1_5147117 31862.08142 . . . . #> chr1_5147118_10294233 . 322.55463 . 158.2779 . #> chr1_10294234_15441350 . . 94.75978 . . #> chr1_15441351_20588466 18864.51846 . 284.27935 . . #> chr1_20588467_25735583 . 806.38658 . . . #> chr1_25735584_30882699 90.26085 80.63866 . . 85.02678 #> #> chr1_1_5147117 143.99885 . . . . . . #> chr1_5147118_10294233 71.99942 . 167.35 . 143.2254 . . #> chr1_10294234_15441350 . 181.3401 . 308.1664 143.2254 . . #> chr1_15441351_20588466 . . . . . 264.2706 . #> chr1_20588467_25735583 . . . . 143.2254 . . #> chr1_25735584_30882699 . . 27278.05 . . . . #> #> chr1_1_5147117 90.72764 66.9927 . . . . #> chr1_5147118_10294233 . . 10613.40465 . . . #> chr1_10294234_15441350 . 66.9927 . . . 80.69722 #> chr1_15441351_20588466 . 66.9927 83.57012 . 118.6944 . #> chr1_20588467_25735583 . . . . . . #> chr1_25735584_30882699 . 11723.7221 . . . . #> #> chr1_1_5147117 . . . . . #> chr1_5147118_10294233 . 98.7947 . 184.0265 . #> chr1_10294234_15441350 . 98.7947 . . . #> chr1_15441351_20588466 68.80418 . . 27143.9087 . #> chr1_20588467_25735583 . 12942.1063 77.93017 . 100.4823 #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 . . #> chr1_5147118_10294233 . . #> chr1_10294234_15441350 . . #> chr1_15441351_20588466 . . #> chr1_20588467_25735583 . 105.921 #> chr1_25735584_30882699 166.1268 .