Find top features for a given assay based on total number of counts for the
feature. Can specify a minimum cell count, or a lower percentile
bound to determine the set of variable features. Running this function will
store the total counts and percentile rank for each feature in the feature
metadata for the assay. To only compute the feature metadata, without
changing the variable features for the assay, set min.cutoff=NA.
FindTopFeatures(object, ...)
# S3 method for default
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)
# S3 method for Assay
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)
# S3 method for StdAssay
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)
# S3 method for Seurat
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)A Seurat object
Arguments passed to other methods
Name of assay to use
Cutoff for feature to be included in the VariableFeatures for the object. This can be a percentile specified as 'q' followed by the minimum percentile, for example 'q5' to set the top 95% most common features as the VariableFeatures for the object. Alternatively, this can be an integer specifying the minimum number of counts for the feature to be included in the set of VariableFeatures. For example, setting to 10 will include features with >10 total counts in the set of VariableFeatures. If NULL, include all features in VariableFeatures. If NA, VariableFeatures will not be altered, and only the feature metadata will be updated with the total counts and percentile rank for each feature.
Display messages
Returns a Seurat object
FindTopFeatures(object = atac_small[['peaks']]['data'])
#> count percentile
#> chr1-2157847-2188813 384.21692 1.000000000
#> chr1-6843960-6846894 306.71972 0.996904025
#> chr1-3815928-3820356 293.92311 0.993808050
#> chr1-2471903-2481288 291.68103 0.990712074
#> chr1-2515241-2519350 273.54125 0.987616099
#> chr1-6051145-6055407 271.58079 0.984520124
#> chr1-6659264-6664388 269.06630 0.981424149
#> chr1-8935313-8940649 257.13518 0.978328173
#> chr1-1549446-1552535 249.25680 0.975232198
#> chr1-8020317-8022548 245.27406 0.972136223
#> chr1-1708510-1715065 238.85121 0.969040248
#> chr1-2322313-2323985 234.97422 0.965944272
#> chr1-3540009-3542500 226.59025 0.962848297
#> chr1-6672613-6675785 224.61335 0.959752322
#> chr1-2343197-2348396 223.27737 0.956656347
#> chr1-2486054-2489237 220.64562 0.953560372
#> chr1-6639159-6642773 220.03083 0.950464396
#> chr1-1051006-1053102 219.01926 0.947368421
#> chr1-1849693-1853920 216.86560 0.944272446
#> chr1-6085254-6089147 209.43368 0.941176471
#> chr1-2063672-2065744 208.40462 0.938080495
#> chr1-1240091-1245762 202.41066 0.934984520
#> chr1-1309645-1311492 200.93170 0.931888545
#> chr1-1333514-1336003 199.69752 0.928792570
#> chr1-1819732-1824104 199.57829 0.925696594
#> chr1-2135022-2137621 198.43822 0.922600619
#> chr1-928630-937949 195.69880 0.919504644
#> chr1-6452328-6454679 194.68799 0.916408669
#> chr1-1839727-1841458 192.45257 0.913312693
#> chr1-7830534-7832331 191.47613 0.910216718
#> chr1-9293115-9295644 188.43304 0.907120743
#> chr1-2125466-2127403 188.28612 0.904024768
#> chr1-7841489-7844891 180.48141 0.900928793
#> chr1-2456987-2458884 178.90723 0.897832817
#> chr1-1446312-1448163 177.61112 0.894736842
#> chr1-9188154-9190941 176.17157 0.891640867
#> chr1-1655226-1656410 175.89464 0.888544892
#> chr1-713460-714823 175.20779 0.885448916
#> chr1-1259506-1261414 172.88999 0.882352941
#> chr1-3773000-3774956 170.91511 0.879256966
#> chr1-1166366-1168282 169.69997 0.876160991
#> chr1-1623610-1625141 167.78231 0.873065015
#> chr1-1341794-1343522 166.82518 0.869969040
#> chr1-1562519-1567986 165.90765 0.866873065
#> chr1-2227715-2234197 163.94501 0.863777090
#> chr1-894021-896898 163.92453 0.860681115
#> chr1-2241757-2247855 162.95554 0.857585139
#> chr1-8876634-8878709 158.30708 0.854489164
#> chr1-6258846-6260407 155.41484 0.851393189
#> chr1-8013637-8014963 153.16873 0.848297214
#> chr1-1509089-1511050 152.49880 0.845201238
#> chr1-1980856-1982929 152.22569 0.842105263
#> chr1-7763862-7766072 150.39382 0.839009288
#> chr1-2573495-2575472 146.91583 0.835913313
#> chr1-954372-958413 144.81406 0.832817337
#> chr1-8584964-8586531 144.25964 0.829721362
#> chr1-2507261-2510518 142.61074 0.826625387
#> chr1-2130011-2131484 141.84665 0.823529412
#> chr1-6613890-6615140 141.29329 0.820433437
#> chr1-2221250-2223390 137.61758 0.817337461
#> chr1-1406028-1408272 137.55682 0.814241486
#> chr1-1283373-1285555 136.39638 0.811145511
#> chr1-8085460-8087248 135.60007 0.808049536
#> chr1-1207999-1210168 134.51559 0.804953560
#> chr1-6684553-6686243 129.16952 0.801857585
#> chr1-1002063-1006231 128.99640 0.798761610
#> chr1-1589986-1591117 126.80636 0.795665635
#> chr1-6761132-6762608 126.40764 0.792569659
#> chr1-994056-995654 125.59260 0.789473684
#> chr1-973840-977754 124.71487 0.786377709
#> chr1-762106-763359 123.17802 0.783281734
#> chr1-948133-951142 122.24861 0.780185759
#> chr1-3712392-3713775 121.80754 0.777089783
#> chr1-2120455-2122065 116.93195 0.773993808
#> chr1-1306174-1308201 113.16641 0.770897833
#> chr1-2082091-2083429 112.73853 0.767801858
#> chr1-3565942-3569718 110.18451 0.764705882
#> chr1-3688192-3690359 109.72059 0.761609907
#> chr1-2143708-2144981 108.88198 0.758513932
#> chr1-1147592-1153647 105.88473 0.755417957
#> chr1-1135873-1137356 105.68426 0.752321981
#> chr1-8482480-8485295 104.61046 0.749226006
#> chr1-6319594-6322140 103.52703 0.746130031
#> chr1-6295272-6296706 100.78740 0.743034056
#> chr1-1092026-1094240 100.73212 0.739938080
#> chr1-3535177-3536355 100.46039 0.736842105
#> chr1-8000672-8003534 99.37711 0.733746130
#> chr1-967806-970136 88.56877 0.730650155
#> chr1-9352328-9354391 86.97476 0.727554180
#> chr1-8762907-8763964 86.29183 0.724458204
#> chr1-6304964-6307369 84.12494 0.721362229
#> chr1-998895-1000200 82.58409 0.718266254
#> chr1-1140204-1144858 82.27853 0.715170279
#> chr1-1057192-1058404 82.26495 0.712074303
#> chr1-1695549-1696821 80.78735 0.708978328
#> chr1-3662633-3664352 74.64851 0.705882353
#> chr1-6418151-6420435 73.54881 0.702786378
#> chr1-8487258-8488478 73.21975 0.699690402
#> chr1-6187544-6188439 72.91401 0.696594427
#> chr1-901313-902847 72.70957 0.693498452
#> chr1-2454600-2456271 72.68043 0.690402477
#> chr1-1534779-1536172 72.49716 0.687306502
#> chr1-3446985-3448712 72.11667 0.684210526
#> chr1-8186838-8187845 71.40895 0.681114551
#> chr1-1800682-1801583 71.11832 0.678018576
#> chr1-2079917-2080950 68.57285 0.674922601
#> chr1-8242128-8243255 66.37742 0.671826625
#> chr1-839520-841123 65.20831 0.668730650
#> chr1-8212306-8213910 65.07565 0.665634675
#> chr1-8933459-8934461 64.85924 0.662538700
#> chr1-3593401-3595956 64.40517 0.659442724
#> chr1-2189545-2192208 64.21689 0.656346749
#> chr1-6507013-6510383 64.12674 0.653250774
#> chr1-2312793-2314371 64.11823 0.650154799
#> chr1-6557001-6558057 62.69369 0.647058824
#> chr1-6519517-6521256 62.20746 0.643962848
#> chr1-804872-805761 61.40569 0.640866873
#> chr1-6523645-6526848 60.91506 0.637770898
#> chr1-9349019-9350779 60.77918 0.634674923
#> chr1-7740033-7741328 59.80320 0.631578947
#> chr1-6407925-6409601 59.46040 0.628482972
#> chr1-6801917-6804384 59.43025 0.625386997
#> chr1-858464-861548 59.12162 0.622291022
#> chr1-3806419-3808097 58.99226 0.619195046
#> chr1-6208425-6209293 58.19203 0.616099071
#> chr1-9335457-9336176 57.50392 0.613003096
#> chr1-9222989-9224547 57.15359 0.609907121
#> chr1-1288121-1291291 56.32419 0.606811146
#> chr1-752422-753038 56.22403 0.603715170
#> chr1-2460345-2462489 55.52539 0.600619195
#> chr1-1975839-1976906 54.86054 0.597523220
#> chr1-8377792-8378947 54.70647 0.594427245
#> chr1-2071091-2071791 54.53793 0.591331269
#> chr1-8760958-8762003 53.45674 0.588235294
#> chr1-6264890-6266821 53.35970 0.585139319
#> chr1-6268667-6270086 50.44472 0.582043344
#> chr1-1014697-1015912 50.02656 0.578947368
#> chr1-3369629-3371833 49.89949 0.575851393
#> chr1-8408802-8409630 49.79611 0.572755418
#> chr1-6115973-6117096 49.69981 0.569659443
#> chr1-2756472-2757468 48.83855 0.566563467
#> chr1-8284654-8285560 48.38582 0.563467492
#> chr1-875427-878705 48.31586 0.560371517
#> chr1-8455220-8456159 47.90883 0.557275542
#> chr1-1071616-1073471 47.66006 0.554179567
#> chr1-9047790-9048521 47.61691 0.551083591
#> chr1-1440010-1441302 47.56794 0.547987616
#> chr1-6545462-6547152 47.41900 0.544891641
#> chr1-3513943-3514649 47.22296 0.541795666
#> chr1-9299648-9300348 46.46411 0.538699690
#> chr1-1837423-1839193 45.96391 0.535603715
#> chr1-7989680-7991862 45.15346 0.532507740
#> chr1-6483424-6485428 44.87202 0.529411765
#> chr1-919270-919976 44.71326 0.526315789
#> chr1-6159426-6161621 44.61020 0.523219814
#> chr1-1369325-1371497 43.62080 0.520123839
#> chr1-1608771-1610748 43.55428 0.517027864
#> chr1-2058137-2059185 42.84766 0.513931889
#> chr1-6549536-6551487 42.84170 0.510835913
#> chr1-5448721-5449698 42.81908 0.507739938
#> chr1-1185856-1186893 42.15297 0.504643963
#> chr1-1706795-1707660 41.47936 0.501547988
#> chr1-1226995-1227705 41.47536 0.498452012
#> chr1-9202229-9203756 41.23368 0.495356037
#> chr1-8918082-8920107 40.45121 0.492260062
#> chr1-2155475-2156839 40.13801 0.489164087
#> chr1-2426847-2429351 38.59664 0.486068111
#> chr1-8555950-8557971 38.59399 0.482972136
#> chr1-6535328-6536188 38.42537 0.479876161
#> chr1-9064752-9065614 38.38522 0.476780186
#> chr1-3527180-3529385 38.26831 0.473684211
#> chr1-8164523-8165144 37.71384 0.470588235
#> chr1-3585229-3585878 37.51411 0.467492260
#> chr1-8772445-8773223 37.38709 0.464396285
#> chr1-2206598-2208283 36.59175 0.461300310
#> chr1-7022276-7023784 36.37719 0.458204334
#> chr1-8035301-8035725 36.01837 0.455108359
#> chr1-1397565-1398360 35.50460 0.452012384
#> chr1-6474354-6474772 35.34273 0.448916409
#> chr1-9129476-9130126 35.30710 0.445820433
#> chr1-1677619-1678941 34.68942 0.442724458
#> chr1-1788464-1789189 34.33025 0.439628483
#> chr1-939991-941002 33.58141 0.436532508
#> chr1-8008972-8009703 33.51396 0.433436533
#> chr1-7962633-7963232 33.43984 0.430340557
#> chr1-8042128-8042915 33.41576 0.427244582
#> chr1-9241288-9242647 33.36153 0.424148607
#> chr1-8448058-8448562 32.80253 0.421052632
#> chr1-6118667-6119050 32.75566 0.417956656
#> chr1-9030034-9031614 32.57688 0.414860681
#> chr1-3537510-3538045 32.53158 0.411764706
#> chr1-8229422-8230556 31.98217 0.408668731
#> chr1-6403422-6403936 31.78621 0.405572755
#> chr1-8277105-8277928 31.44905 0.402476780
#> chr1-9170725-9171256 31.20174 0.399380805
#> chr1-1542207-1543000 31.01101 0.396284830
#> chr1-6464664-6465176 30.93889 0.393188854
#> chr1-6074646-6075340 30.87746 0.390092879
#> chr1-1927576-1928068 30.80053 0.386996904
#> chr1-2105657-2106319 30.67876 0.383900929
#> chr1-7727502-7728223 30.07156 0.380804954
#> chr1-6500054-6501132 29.97548 0.377708978
#> chr1-9070978-9072039 29.81707 0.374613003
#> chr1-9256287-9256980 29.77762 0.371517028
#> chr1-2843088-2844374 29.55906 0.368421053
#> chr1-6461699-6462218 29.52764 0.365325077
#> chr1-9134957-9135502 29.52764 0.362229102
#> chr1-8278622-8279253 29.43471 0.359133127
#> chr1-1772973-1773995 29.32932 0.356037152
#> chr1-7788851-7789256 29.31657 0.352941176
#> chr1-3710108-3710711 29.17940 0.349845201
#> chr1-7812830-7814063 29.04675 0.346749226
#> chr1-8959709-8960452 29.02094 0.343653251
#> chr1-779589-780271 28.93765 0.340557276
#> chr1-8978053-8978591 28.90584 0.337461300
#> chr1-8570017-8570771 28.85912 0.334365325
#> chr1-6779996-6780494 28.84395 0.331269350
#> chr1-8723942-8724565 28.32633 0.328173375
#> chr1-3407512-3408483 28.15516 0.325077399
#> chr1-1780695-1781014 27.90953 0.321981424
#> chr1-1475360-1476487 27.90201 0.318885449
#> chr1-1034158-1035389 27.71969 0.315789474
#> chr1-2430822-2432046 27.64848 0.312693498
#> chr1-7729458-7730117 27.24362 0.309597523
#> chr1-3481736-3482215 26.96688 0.306501548
#> chr1-911152-912038 25.87086 0.303405573
#> chr1-6061422-6063389 25.59549 0.300309598
#> chr1-6497838-6498680 25.50923 0.297213622
#> chr1-3838659-3839297 25.48883 0.294117647
#> chr1-8156770-8157834 25.42064 0.291021672
#> chr1-3640902-3641383 25.25429 0.287925697
#> chr1-8951785-8952241 24.97391 0.284829721
#> chr1-2074156-2074747 24.64233 0.281733746
#> chr1-8931013-8932013 24.48537 0.278637771
#> chr1-1617619-1618183 24.34439 0.275541796
#> chr1-1804025-1804468 23.92381 0.272445820
#> chr1-6949969-6950349 23.56573 0.269349845
#> chr1-3232972-3233779 23.36809 0.266253870
#> chr1-1812400-1813494 23.29113 0.263157895
#> chr1-1690269-1690749 23.28698 0.260061920
#> chr1-8456996-8458096 23.17583 0.256965944
#> chr1-8689375-8690307 22.83893 0.253869969
#> chr1-925760-926165 22.71872 0.250773994
#> chr1-2043788-2044372 22.70338 0.247678019
#> chr1-944476-944998 22.60427 0.244582043
#> chr1-6425029-6425683 22.43174 0.241486068
#> chr1-8467741-8468104 22.21124 0.238390093
#> chr1-8075007-8075497 22.06632 0.235294118
#> chr1-1597084-1597513 21.92619 0.232198142
#> chr1-1817581-1818125 21.81084 0.229102167
#> chr1-1154588-1155301 21.51467 0.226006192
#> chr1-6706469-6707017 21.33187 0.222910217
#> chr1-8523212-8523742 21.30277 0.219814241
#> chr1-1532974-1533319 21.24422 0.216718266
#> chr1-1789961-1790535 21.07197 0.213622291
#> chr1-6065317-6066074 20.87407 0.210526316
#> chr1-8442858-8443649 20.58893 0.207430341
#> chr1-1361935-1362825 20.52874 0.204334365
#> chr1-5726874-5727812 20.39156 0.201238390
#> chr1-1108888-1109641 20.16466 0.198142415
#> chr1-1727875-1728288 20.11176 0.195046440
#> chr1-3827263-3827968 19.83199 0.191950464
#> chr1-9181580-9182573 19.82025 0.188854489
#> chr1-6112490-6113074 19.79287 0.185758514
#> chr1-6072846-6073562 19.61238 0.182662539
#> chr1-2236104-2237259 18.81426 0.179566563
#> chr1-1079247-1080264 18.60463 0.176470588
#> chr1-9153374-9153983 18.53070 0.173374613
#> chr1-7975875-7976274 18.47008 0.170278638
#> chr1-3759680-3759895 18.20419 0.167182663
#> chr1-9161610-9161990 17.80685 0.164086687
#> chr1-9143106-9143741 17.70684 0.160990712
#> chr1-8469105-8469816 17.69342 0.157894737
#> chr1-3692008-3692971 17.65533 0.154798762
#> chr1-6651141-6652061 17.65161 0.151702786
#> chr1-2077596-2078445 17.59963 0.148606811
#> chr1-8685625-8685837 17.51682 0.145510836
#> chr1-9191514-9192075 17.49105 0.142414861
#> chr1-9327071-9327557 17.40802 0.139318885
#> chr1-9006466-9007566 17.29060 0.136222910
#> chr1-8166762-8167329 17.21747 0.133126935
#> chr1-8621060-8621547 17.14415 0.130030960
#> chr1-9239865-9240117 17.05492 0.126934985
#> chr1-3612122-3612609 17.02228 0.123839009
#> chr1-5541924-5542287 16.99673 0.120743034
#> chr1-6094452-6094929 16.85274 0.117647059
#> chr1-2585232-2586236 16.66483 0.114551084
#> chr1-6787479-6787943 16.62420 0.111455108
#> chr1-8498906-8499422 16.58999 0.108359133
#> chr1-1729436-1729707 16.57089 0.105263158
#> chr1-1814487-1815655 16.55285 0.102167183
#> chr1-8374335-8374807 16.43022 0.099071207
#> chr1-2046611-2047074 16.41455 0.095975232
#> chr1-6158309-6158535 16.37715 0.092879257
#> chr1-8786544-8786946 16.26625 0.089783282
#> chr1-1553343-1553743 16.13808 0.086687307
#> chr1-1337323-1337799 16.04696 0.083591331
#> chr1-8986755-8987690 16.03087 0.080495356
#> chr1-1891426-1891854 16.01805 0.077399381
#> chr1-1797303-1797631 16.00534 0.074303406
#> chr1-2949388-2950228 15.95259 0.071207430
#> chr1-1293753-1295053 15.94474 0.068111455
#> chr1-9046821-9047245 15.89577 0.065015480
#> chr1-2489999-2490171 15.73654 0.061919505
#> chr1-2425108-2425944 15.72151 0.058823529
#> chr1-1875345-1875801 15.46934 0.055727554
#> chr1-7846855-7847243 15.35028 0.052631579
#> chr1-1660021-1660414 15.18657 0.049535604
#> chr1-6514584-6515741 15.12015 0.046439628
#> chr1-4066997-4068144 15.08596 0.043343653
#> chr1-2068827-2069139 14.89973 0.040247678
#> chr1-8227330-8227690 14.80640 0.037151703
#> chr1-3546738-3547139 14.74907 0.034055728
#> chr1-856165-857031 14.69076 0.030959752
#> chr1-2513019-2513577 14.61441 0.027863777
#> chr1-2023023-2023435 14.26935 0.024767802
#> chr1-4712641-4713007 14.11462 0.021671827
#> chr1-3703815-3704555 14.02232 0.018575851
#> chr1-2398568-2399841 13.85986 0.015479876
#> chr1-841866-842572 13.15817 0.012383901
#> chr1-2703118-2703609 13.06000 0.009287926
#> chr1-8580547-8580902 12.94360 0.006191950
#> chr1-3799784-3800744 12.33028 0.003095975
FindTopFeatures(object = atac_small[['peaks']])
#> ChromatinAssay data with 323 features for 100 cells
#> Variable features: 314
#> Genome: hg19
#> Annotation present: TRUE
#> Motifs present: TRUE
#> Fragment files: 0
FindTopFeatures(object = atac_small[['peaks']])
#> ChromatinAssay data with 323 features for 100 cells
#> Variable features: 314
#> Genome: hg19
#> Annotation present: TRUE
#> Motifs present: TRUE
#> Fragment files: 0
FindTopFeatures(atac_small)
#> An object of class Seurat
#> 1323 features across 100 samples within 3 assays
#> Active assay: peaks (323 features, 314 variable features)
#> 2 layers present: counts, data
#> 2 other assays present: bins, RNA
#> 2 dimensional reductions calculated: lsi, umap