Normalize counts
normalize_scExp( scExp, type = c("CPM", "TFIDF", "RPKM", "TPM", "feature_size_only") )
| scExp | A SingleCellExperiment object. |
|---|---|
| type | Which normalization to apply. Either 'CPM', 'TFIDF','RPKM', 'TPM' or 'feature_size_only'. Note that for all normalization by size (RPKM, TPM, feature_size_only), the features must have defined genomic coordinates. |
A SingleCellExperiment object containing normalized counts. (See ?normcounts())
#>#> 6 x 300 sparse Matrix of class "dgCMatrix"#>#> #> chr1_1_5147117 . . . 36368.89832 . . #> chr1_5147118_10294233 . . 160.5008 96.46923 . . #> chr1_10294234_15441350 13760.4 115.9689 . . . . #> chr1_15441351_20588466 . . . . . 77.61565 #> chr1_20588467_25735583 . 115.9689 160.5008 96.46923 . . #> chr1_25735584_30882699 . . . . . 77.61565 #> #> chr1_1_5147117 . . . 108.4716 . 84.91127 #> chr1_5147118_10294233 21687.8831 68.5824 . . . . #> chr1_10294234_15441350 188.5903 . . . . . #> chr1_15441351_20588466 . 137.1648 . 108.4716 . . #> chr1_20588467_25735583 . 8229.8882 6625.564 108.4716 . . #> chr1_25735584_30882699 . . . . . . #> #> chr1_1_5147117 . . . 87.83487 . #> chr1_5147118_10294233 82.68563 7524.38458 87.98944 . . #> chr1_10294234_15441350 . . 175.97888 . . #> chr1_15441351_20588466 . . 87.98944 . . #> chr1_20588467_25735583 82.68563 92.89364 27540.69512 175.66974 . #> chr1_25735584_30882699 . . . . 111.0741 #> #> chr1_1_5147117 . . . . . . #> chr1_5147118_10294233 . . 88.56611 . . 34267.62 #> chr1_10294234_15441350 138.85032 . 2479.85121 . . . #> chr1_15441351_20588466 5068.03666 103.509 88.56611 . . . #> chr1_20588467_25735583 69.42516 . 19130.28075 . 173.1752 . #> chr1_25735584_30882699 28047.76451 . 13904.87999 . . . #> #> chr1_1_5147117 . . 90.70295 . . #> chr1_5147118_10294233 . 77.56748 . . . #> chr1_10294234_15441350 86.87343 . 11428.57143 17546.89 . #> chr1_15441351_20588466 . 10937.01520 32380.95238 . 77.30963 #> chr1_20588467_25735583 86.87343 77.56748 . . . #> chr1_25735584_30882699 173.74685 . . 12360.62 2396.59838 #> #> chr1_1_5147117 . . 249.56326 88.16787 86.26639 #> chr1_5147118_10294233 69.04647 . 83.18775 176.33574 . #> chr1_10294234_15441350 . . . . . #> chr1_15441351_20588466 . 87.86574 249.56326 . 86.26639 #> chr1_20588467_25735583 . . 83.18775 . . #> chr1_25735584_30882699 . . . 88.16787 86.26639 #> #> chr1_1_5147117 . . . 134.7709 . 85.5432 #> chr1_5147118_10294233 89.03134 . . . . . #> chr1_10294234_15441350 178.06268 90.62897 . . 230.9647 85.5432 #> chr1_15441351_20588466 178.06268 . . . . 171.0864 #> chr1_20588467_25735583 20566.23932 . . 202.1563 . 85.5432 #> chr1_25735584_30882699 89.03134 . . 16711.5903 . . #> #> chr1_1_5147117 . . . 167.29402 9974.853 . #> chr1_5147118_10294233 . . . 250.94103 . 10800.72005 #> chr1_10294234_15441350 . 397.9044 . . . . #> chr1_15441351_20588466 . 5305.3916 . 83.64701 . 66.67111 #> chr1_20588467_25735583 84.81045 . . 4182.35048 . . #> chr1_25735584_30882699 . 10876.0528 . 167.29402 . 66.67111 #> #> chr1_1_5147117 193.8548 86.58758 . . . #> chr1_5147118_10294233 . . 214.064 . 19414.5458 #> chr1_10294234_15441350 . 173.17517 321.096 . . #> chr1_15441351_20588466 . . 107.032 . . #> chr1_20588467_25735583 . . . . . #> chr1_25735584_30882699 . 173.17517 . 91.29919 100.5935 #> #> chr1_1_5147117 . . . . 215.8429 . #> chr1_5147118_10294233 23661.38763 149.7903 . . . . #> chr1_10294234_15441350 94.26848 . . 96.24639 107.9214 . #> chr1_15441351_20588466 . . 76.94675 . . . #> chr1_20588467_25735583 . . 76.94675 . 107.9214 80.94544 #> chr1_25735584_30882699 . . . 96.24639 . . #> #> chr1_1_5147117 12350.83034 . . . . #> chr1_5147118_10294233 . 154.703 . . . #> chr1_10294234_15441350 83.45156 . 4999.55361 10362.69430 . #> chr1_15441351_20588466 . . . 72.97672 . #> chr1_20588467_25735583 . . . . . #> chr1_25735584_30882699 83.45156 . 89.27774 . 82.17602 #> #> chr1_1_5147117 21820.21634 . . . . #> chr1_5147118_10294233 26855.65088 91.85267 . 92.04713 . #> chr1_10294234_15441350 . . 98.39614 . 194.5021 #> chr1_15441351_20588466 93.24879 91.85267 98.39614 . 12642.6349 #> chr1_20588467_25735583 . 91.85267 . 92.04713 . #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 . . . . 170.69216 #> chr1_5147118_10294233 . 80.07046 82.08159 71.50007 . #> chr1_10294234_15441350 . 80.07046 . 71.50007 85.34608 #> chr1_15441351_20588466 90.90083 . . 1072.50107 . #> chr1_20588467_25735583 6635.76039 . . 11654.51165 . #> chr1_25735584_30882699 . . 328.32636 143.00014 . #> #> chr1_1_5147117 85.12812 83.09098 . 156.9366 . #> chr1_5147118_10294233 85.12812 83.09098 . . 10821.77883 #> chr1_10294234_15441350 . . 157.30691 . 84.54515 #> chr1_15441351_20588466 85.12812 14291.64936 . . . #> chr1_20588467_25735583 . . 78.65345 . 84.54515 #> chr1_25735584_30882699 . . 78.65345 . . #> #> chr1_1_5147117 18846.22191 . 87.64242 . . #> chr1_5147118_10294233 24597.41639 92.45562 . 191.18631 . #> chr1_10294234_15441350 . . . . . #> chr1_15441351_20588466 . . . 95.59316 469.9984 #> chr1_20588467_25735583 . . . . . #> chr1_25735584_30882699 88.47992 92.45562 . . . #> #> chr1_1_5147117 84.2531 217.4149 106.849 . . . #> chr1_5147118_10294233 . 108.7075 106.849 . . . #> chr1_10294234_15441350 168.5062 . . 77.33354 . 232.3150 #> chr1_15441351_20588466 252.7593 . . . . . #> chr1_20588467_25735583 28730.3058 108.7075 . . . . #> chr1_25735584_30882699 . 108.7075 49898.493 77.33354 5045.91 116.1575 #> #> chr1_1_5147117 9585.5395 . . . . #> chr1_5147118_10294233 182.5817 222.354 9253.4992 . . #> chr1_10294234_15441350 . 26460.125 77.7605 19033.80767 . #> chr1_15441351_20588466 . 74.118 . 90.63718 84.70269 #> chr1_20588467_25735583 . 74.118 12441.6796 181.27436 84.70269 #> chr1_25735584_30882699 . . . 90.63718 . #> #> chr1_1_5147117 . . . 20963.87 . #> chr1_5147118_10294233 . 247.4635 . . 83.70302 #> chr1_10294234_15441350 . . . . . #> chr1_15441351_20588466 167.6024 . . 16477.14 . #> chr1_20588467_25735583 15000.4190 123.7317 317.8387 . 83.70302 #> chr1_25735584_30882699 . 123.7317 . . . #> #> chr1_1_5147117 . 80.69071 23231.42696 . . #> chr1_5147118_10294233 78.27176 . . . . #> chr1_10294234_15441350 . 80.69071 . 72.74314 192.1968 #> chr1_15441351_20588466 . 80.69071 . 72.74314 96.0984 #> chr1_20588467_25735583 . . 4275.22788 . 26138.7661 #> chr1_25735584_30882699 4696.30557 . 80.66468 72.74314 . #> #> chr1_1_5147117 . . . . . . #> chr1_5147118_10294233 . . 70.75138 260.5184 148.6768 . #> chr1_10294234_15441350 236.79848 . . . 9217.9602 11635.08 #> chr1_15441351_20588466 78.93283 . 22781.94425 260.5184 . . #> chr1_20588467_25735583 . . . . 9143.6218 . #> chr1_25735584_30882699 157.86566 . . . . 17276.33 #> #> chr1_1_5147117 87.28288 48438.8678 113.7268 . 141.6832 #> chr1_5147118_10294233 . 97.2668 . 34790.2783 70.8416 #> chr1_10294234_15441350 . . . . . #> chr1_15441351_20588466 . 19939.6946 113.7268 . . #> chr1_20588467_25735583 . 194.5336 . 294.0024 70.8416 #> chr1_25735584_30882699 . . . . 70.8416 #> #> chr1_1_5147117 . . . 189.53753 . . . #> chr1_5147118_10294233 88.95214 . . . . . . #> chr1_10294234_15441350 88.95214 . . 94.76876 14698.71125 . 156.05493 #> chr1_15441351_20588466 . . . . 69.66214 . 78.02747 #> chr1_20588467_25735583 88.95214 . . 94.76876 . 14921.8566 . #> chr1_25735584_30882699 . . . 189.53753 . 157.0722 . #> #> chr1_1_5147117 . . 188.53695 . 91.37427 #> chr1_5147118_10294233 . . . 291.1773 . #> chr1_10294234_15441350 97.15341 . . . . #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 97.15341 14860.07916 94.26848 . . #> chr1_25735584_30882699 97.15341 69.43962 94.26848 . 14437.13450 #> #> chr1_1_5147117 . . . 5922.6112 160.75878 #> chr1_5147118_10294233 . 116.9864 . 131.6136 80.37939 #> chr1_10294234_15441350 261.94010 . 665.6523 9147.1440 . #> chr1_15441351_20588466 . . 190.1864 . 80.37939 #> chr1_20588467_25735583 87.31337 . . . 80.37939 #> chr1_25735584_30882699 . . . 16517.5046 80.37939 #> #> chr1_1_5147117 111.2842 171.8065 121.9289 1355.35790 . #> chr1_5147118_10294233 111.2842 . . 84.70987 91.88643 #> chr1_10294234_15441350 111.2842 . . 84.70987 91.88643 #> chr1_15441351_20588466 222.5684 . 5669.6946 . . #> chr1_20588467_25735583 . . . . 91.88643 #> chr1_25735584_30882699 11128.4220 . . . 183.77286 #> #> chr1_1_5147117 . . 84.40243 118.3572 2730.642 #> chr1_5147118_10294233 . 296.82398 84.40243 19528.9383 . #> chr1_10294234_15441350 550.96419 98.94133 . . 9459.723 #> chr1_15441351_20588466 91.82736 . 168.80486 . . #> chr1_20588467_25735583 . 197.88266 . . . #> chr1_25735584_30882699 91.82736 . . . . #> #> chr1_1_5147117 4038.0733 128.1230 . 76.15566 883.39223 #> chr1_5147118_10294233 . . 62.0155 . 1325.08834 #> chr1_10294234_15441350 . 64.0615 . 76.15566 . #> chr1_15441351_20588466 96.1446 . . . 88.33922 #> chr1_20588467_25735583 . 4740.5509 . 17591.95796 . #> chr1_25735584_30882699 . 64.0615 62.0155 . . #> #> chr1_1_5147117 . 95.8589 88.89679 92.19989 . #> chr1_5147118_10294233 . 95.8589 . . . #> chr1_10294234_15441350 . 16583.5890 177.79358 . . #> chr1_15441351_20588466 . . . . 177.0695 #> chr1_20588467_25735583 82.47423 95.8589 5689.39461 . . #> chr1_25735584_30882699 . . 177.79358 92.19989 . #> #> chr1_1_5147117 . . . 109.218 . #> chr1_5147118_10294233 . 80.17317 . . . #> chr1_10294234_15441350 170.76503 . 5932.97692 . 75.80352 #> chr1_15441351_20588466 1707.65027 160.34635 . 109.218 . #> chr1_20588467_25735583 85.38251 . 65.19755 218.436 . #> chr1_25735584_30882699 16564.20765 . . . . #> #> chr1_1_5147117 . 16685.10324 79.60516 73.52401 . . . #> chr1_5147118_10294233 . 92.18289 . . . . . #> chr1_10294234_15441350 276.7272 . 159.21032 73.52401 90.84302 . . #> chr1_15441351_20588466 . . 159.21032 . 181.68605 . . #> chr1_20588467_25735583 . . 79.60516 . . . . #> chr1_25735584_30882699 . 19542.77286 . . . . . #> #> chr1_1_5147117 . 160.4750 . 83.62602 . #> chr1_5147118_10294233 85.6898 35304.5013 . . . #> chr1_10294234_15441350 . . 91.10787 . 340.8026 #> chr1_15441351_20588466 . . 91.10787 . 255.6019 #> chr1_20588467_25735583 . 80.2375 91.10787 . . #> chr1_25735584_30882699 . . . 250.87807 . #> #> chr1_1_5147117 90.09821 77.82101 . . . #> chr1_5147118_10294233 13334.53464 155.64202 . 102.976 . #> chr1_10294234_15441350 . . 298.0626 . 177.77778 #> chr1_15441351_20588466 . 20700.38911 99.3542 . 88.88889 #> chr1_20588467_25735583 . . 99.3542 . 266.66667 #> chr1_25735584_30882699 . 155.64202 41033.2837 102.976 11644.44444 #> #> chr1_1_5147117 . . . . . . #> chr1_5147118_10294233 10495.9868 83.09789 13658.5366 273.82256 . . #> chr1_10294234_15441350 205.8037 . 177.3836 . 156.875 . #> chr1_15441351_20588466 . . . 182.54838 . . #> chr1_20588467_25735583 . 3074.62190 . . . . #> chr1_25735584_30882699 205.8037 166.19578 . 91.27419 . . #> #> chr1_1_5147117 . 132.94337 91.67583 3096.86712 . 112.7142 #> chr1_5147118_10294233 . 66.47168 30253.02530 72.02017 . . #> chr1_10294234_15441350 8294.4940 66.47168 12101.21012 40403.31293 . . #> chr1_15441351_20588466 157.9904 . . 11739.28700 . . #> chr1_20588467_25735583 315.9807 . 183.35167 . . . #> chr1_25735584_30882699 13350.1856 . 91.67583 7274.03673 . . #> #> chr1_1_5147117 . 82.22332 92.73857 . . #> chr1_5147118_10294233 . 82.22332 . . . #> chr1_10294234_15441350 . . . 16740.44 . #> chr1_15441351_20588466 32351.99 . . . 73.00336 #> chr1_20588467_25735583 . . . . 73.00336 #> chr1_25735584_30882699 14774.08 10524.58477 . . . #> #> chr1_1_5147117 17416.7387 128.9408 . 81.02415 . #> chr1_5147118_10294233 199.4283 . 74.985 . . #> chr1_10294234_15441350 15754.8361 . 74.985 162.04829 . #> chr1_15441351_20588466 . 18760.8794 74.985 . . #> chr1_20588467_25735583 . . . . 18726.28 #> chr1_25735584_30882699 132.9522 . . . . #> #> chr1_1_5147117 . . 79.20165 . . . #> chr1_5147118_10294233 6312.135 . . . 162.46954 8586.975 #> chr1_10294234_15441350 15701.436 . . . . . #> chr1_15441351_20588466 . . 79.20165 . . . #> chr1_20588467_25735583 34085.529 . . 7753.964 . . #> chr1_25735584_30882699 16332.650 . . . 81.23477 . #> #> chr1_1_5147117 . . 157.5548 89.50148 83.80825 #> chr1_5147118_10294233 210.9705 81.63265 . . . #> chr1_10294234_15441350 . 81.63265 . . 34109.95642 #> chr1_15441351_20588466 . 81.63265 472.6643 . 167.61649 #> chr1_20588467_25735583 210.9705 . . . . #> chr1_25735584_30882699 . 81.63265 . . . #> #> chr1_1_5147117 152.31132 . 15321.15498 . . . . #> chr1_5147118_10294233 . . . . . . . #> chr1_10294234_15441350 . 14741.6 . . . 77.78469 . #> chr1_15441351_20588466 76.15566 . . . . 155.56938 . #> chr1_20588467_25735583 . . 84.18217 . . 155.56938 . #> chr1_25735584_30882699 12261.06161 . 17173.16272 90.10633 . 77.78469 . #> #> chr1_1_5147117 86.50519 51102.20441 . 76.13247 . #> chr1_5147118_10294233 . 91.09127 . . 256.7394 #> chr1_10294234_15441350 . . 88.41733 . . #> chr1_15441351_20588466 86.50519 . . 152.26494 . #> chr1_20588467_25735583 86.50519 . 88.41733 . . #> chr1_25735584_30882699 . . . 228.39741 . #> #> chr1_1_5147117 101.7915 . 72.64274 . . #> chr1_5147118_10294233 . 14378.08406 . 153.68065 78.13721 #> chr1_10294234_15441350 . . 217.92823 76.84033 . #> chr1_15441351_20588466 305.3746 85.07742 . . . #> chr1_20588467_25735583 101.7915 . 72.64274 18364.83787 156.27442 #> chr1_25735584_30882699 101.7915 . . 153.68065 28363.80684 #> #> chr1_1_5147117 75.32957 . . . 89.70219 #> chr1_5147118_10294233 . 117.5364 . 305.6858 10764.26265 #> chr1_10294234_15441350 . 4701.4575 . . . #> chr1_15441351_20588466 . . 13134.13233 . . #> chr1_20588467_25735583 . . 82.08833 203.7905 . #> chr1_25735584_30882699 . 235.0729 . 101.8953 . #> #> chr1_1_5147117 12700.11627 71.93727 . . 97.67533 #> chr1_5147118_10294233 89.43744 143.87454 . . . #> chr1_10294234_15441350 . . 88.96006 . . #> chr1_15441351_20588466 89.43744 71.93727 . . . #> chr1_20588467_25735583 . . 88.96006 . . #> chr1_25735584_30882699 . . . 226.0398 . #> #> chr1_1_5147117 . 169.9524 85.38251 . . #> chr1_5147118_10294233 11778.5630 . 17759.56284 . . #> chr1_10294234_15441350 . 169.9524 . 10156.73 . #> chr1_15441351_20588466 . . 170.76503 . . #> chr1_20588467_25735583 235.5713 29571.7199 256.14754 . 92.48983 #> chr1_25735584_30882699 . . . . . #> #> chr1_1_5147117 . 149.58863 84.06894 . . . #> chr1_5147118_10294233 . 74.79432 . . 10003.57270 . #> chr1_10294234_15441350 270.97823 . . . 178.63523 148.7652 #> chr1_15441351_20588466 90.32608 149.58863 . . 89.31761 2826.5397 #> chr1_20588467_25735583 90.32608 . 84.06894 . . . #> chr1_25735584_30882699 90.32608 14210.91997 168.13787 . . . #> #> chr1_1_5147117 . 357.8458 . . 4693.8776 . #> chr1_5147118_10294233 . 7783.1455 . 83.33333 102.0408 18632.5719 #> chr1_10294234_15441350 . . . . 102.0408 . #> chr1_15441351_20588466 . . 84.94012 . . . #> chr1_20588467_25735583 90.269 . 84.94012 . . 155.9211 #> chr1_25735584_30882699 90.269 . . 83.33333 . . #> #> chr1_1_5147117 31117.87587 . . . . #> chr1_5147118_10294233 84.55945 . . . . #> chr1_10294234_15441350 . . . 93.12721 81.67266 #> chr1_15441351_20588466 84.55945 . . 93.12721 . #> chr1_20588467_25735583 84.55945 64.65796 159.8465 . 163.34531 #> chr1_25735584_30882699 10823.60900 . 159.8465 . . #> #> chr1_1_5147117 . . . . 225.6827 #> chr1_5147118_10294233 . 218.6509 . . . #> chr1_10294234_15441350 . 2733.1365 . . 39043.1054 #> chr1_15441351_20588466 151.1487 28315.2946 77.97271 . . #> chr1_20588467_25735583 . 109.3255 . . . #> chr1_25735584_30882699 24183.7969 . 155.94542 78.69678 25276.4613 #> #> chr1_1_5147117 85.94757 . 83.99126 . . #> chr1_5147118_10294233 23979.37258 114.9822 . 98.31875 . #> chr1_10294234_15441350 171.89514 114.9822 . . 107.2961 #> chr1_15441351_20588466 . . . . 107.2961 #> chr1_20588467_25735583 16244.09110 . . 196.63750 107.2961 #> chr1_25735584_30882699 171.89514 . . . . #> #> chr1_1_5147117 2131.06020 . 238.5686 . . #> chr1_5147118_10294233 . . . . . #> chr1_10294234_15441350 76.10929 . 5009.9404 240.92515 . #> chr1_15441351_20588466 . . . . . #> chr1_20588467_25735583 . 84.50228 . 80.30838 95.09319 #> chr1_25735584_30882699 . 84.50228 . . . #> #> chr1_1_5147117 . 98.84353 182.5484 . . #> chr1_5147118_10294233 . . 182.5484 . . #> chr1_10294234_15441350 . . . 72.0513 . #> chr1_15441351_20588466 22535.2113 . . 19670.0050 11244.84 #> chr1_20588467_25735583 11484.2904 . . . . #> chr1_25735584_30882699 216.6847 . 273.8226 144.1026 14319.60 #> #> chr1_1_5147117 . . 29394.90707 . . #> chr1_5147118_10294233 . 55.8909 81.87996 68.44159 . #> chr1_10294234_15441350 17038.29913 16599.5976 . . . #> chr1_15441351_20588466 . . 11790.71481 136.88317 . #> chr1_20588467_25735583 74.07956 . . 9924.02984 165.9338 #> chr1_25735584_30882699 74.07956 . . . . #> #> chr1_1_5147117 24562.9762 . . . 110.595 #> chr1_5147118_10294233 . . 74.4103 73.04068 110.595 #> chr1_10294234_15441350 1792.9180 89.02341 148.8206 . . #> chr1_15441351_20588466 268.9377 . . . 110.595 #> chr1_20588467_25735583 179.2918 178.04683 . . 110.595 #> chr1_25735584_30882699 89.6459 . 148.8206 . 221.190 #> #> chr1_1_5147117 12027.6380 . 96.18159 . . #> chr1_5147118_10294233 . . . . 103.8098 #> chr1_10294234_15441350 . 81.66599 . 271.1742 103.8098 #> chr1_15441351_20588466 . . 192.36318 . . #> chr1_20588467_25735583 170.6048 163.33197 . . . #> chr1_25735584_30882699 32244.3061 81.66599 . . 207.6196 #> #> chr1_1_5147117 . . 81.27438 6595.01710 . #> chr1_5147118_10294233 132.91686 . . . 177.57258 #> chr1_10294234_15441350 66.45843 . . . . #> chr1_15441351_20588466 . 175.53098 . 81.41996 16603.03649 #> chr1_20588467_25735583 . . . . 88.78629 #> chr1_25735584_30882699 . 87.76549 . . 88.78629 #> #> chr1_1_5147117 . . . 177.10086 96.0984 . #> chr1_5147118_10294233 83.06338 . . . . 195.8864 #> chr1_10294234_15441350 . 96.965 85.64577 . . . #> chr1_15441351_20588466 83.06338 25307.864 . 88.55043 . 391.7728 #> chr1_20588467_25735583 . . . . . . #> chr1_25735584_30882699 . . . . 8456.6596 .