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 Seurat
FindTopFeatures(object, assay = NULL, min.cutoff = "q5", verbose = TRUE, ...)

Arguments

object

A Seurat object

...

Arguments passed to other methods

assay

Name of assay to use

min.cutoff

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 cells containing the feature for the feature to be included in the set of VariableFeatures. For example, setting to 10 will include features in >10 cells 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.

verbose

Display messages

Value

Returns a Seurat object

Examples

FindTopFeatures(object = atac_small[['peaks']][])
#>                          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(atac_small)
#> An object of class Seurat 
#> 1323 features across 100 samples within 3 assays 
#> Active assay: peaks (323 features, 314 variable features)
#>  2 other assays present: bins, RNA
#>  2 dimensional reductions calculated: lsi, umap