R/AllGenerics.R, R/pseudo_samples-methods.R
pseudo_samples.RdGather cells for each group according to specified factors, then randomly assign and aggregate cells to each pseudo-samples with randomized cell size. (min.cells <= size <= max.cells)
pseudo_samples(
data,
by,
fun = c("sum", "mean"),
scale = NULL,
min.cells = 0,
max.cells = Inf,
slot = "counts"
)
# S4 method for matrix,data.frame
pseudo_samples(
data,
by,
fun = c("sum", "mean"),
scale = NULL,
min.cells = 0,
max.cells = Inf,
slot = "counts"
)
# S4 method for matrix,vector
pseudo_samples(
data,
by,
fun = c("sum", "mean"),
scale = NULL,
min.cells = 0,
max.cells = Inf,
slot = "counts"
)
# S4 method for Seurat,character
pseudo_samples(
data,
by,
fun = c("sum", "mean"),
scale = NULL,
min.cells = 0,
max.cells = Inf,
slot = "counts"
)
# S4 method for SummarizedExperiment,character
pseudo_samples(
data,
by,
fun = c("sum", "mean"),
scale = NULL,
min.cells = 0,
max.cells = Inf,
slot = "counts"
)a matrix or Seurat/SCE object containing expression and metadata
a vector of group names or dataframe for aggregation
chr, methods used to aggregate cells, could be 'sum' or 'mean', default 'sum'
a num or NULL, if to multiply a scale to the average expression
num, default 300, the minimum size of cells aggregating to each pseudo-sample
num, default 600, the maximum size of cells aggregating to each pseudo-sample
chr, specify which slot of seurat object to aggregate, can be 'counts', 'data', 'scale.data'..., default is 'counts'
An expression matrix after aggregating cells on specified factors
counts <- matrix(abs(rnorm(10000, 10, 10)), 100)
rownames(counts) <- 1:100
colnames(counts) <- 1:100
meta <- data.frame(
subset = rep(c("A", "B"), 50),
level = rep(1:4, each = 25)
)
rownames(meta) <- 1:100
scRNA <- SeuratObject::CreateSeuratObject(counts = counts, meta.data = meta)
#> Warning: Data is of class matrix. Coercing to dgCMatrix.
pseudo_samples(scRNA,
by = c("subset", "level"),
min.cells = 10, max.cells = 20
)
#> A.1_1 B.1_1 A.2_1 B.2_1 A.3_1 B.3_1 A.4_1
#> 1 189.68722 121.98300 173.59774 132.37316 161.90622 82.83385 74.00843
#> 2 113.55731 143.13743 149.34681 135.02673 118.68681 105.62701 180.36954
#> 3 131.75680 120.33109 88.79949 136.70885 127.87282 113.85903 103.15364
#> 4 137.79398 123.99236 104.62808 170.11164 167.21097 133.73793 96.14825
#> 5 119.70122 155.69769 95.49198 158.68897 157.32530 164.67492 148.26891
#> 6 142.84524 91.72708 165.75720 153.66090 157.42112 141.95432 163.26024
#> 7 135.35171 63.31922 159.55743 165.07608 127.54185 126.04112 144.15204
#> 8 167.63501 113.18236 176.09361 148.38489 132.46825 131.80872 146.52483
#> 9 125.49418 174.31157 201.61424 132.20680 184.64838 171.16434 130.79296
#> 10 151.14669 130.48577 74.25771 170.67381 208.84564 109.02682 112.01205
#> 11 141.28966 105.18412 111.67373 153.81897 146.44124 109.66240 161.11279
#> 12 133.02632 112.49485 141.66453 133.54187 139.52859 102.35169 153.01657
#> 13 211.98352 103.69540 196.75709 111.52534 135.98126 181.67306 136.81369
#> 14 161.54498 95.64675 128.72895 185.88465 142.49943 88.60712 207.66124
#> 15 181.50221 145.34465 175.52367 155.39052 132.69363 125.83006 152.05919
#> 16 139.76634 170.28360 144.04753 115.58868 94.30047 139.03152 158.27809
#> 17 119.25600 122.25930 106.82541 210.47899 159.34706 172.30329 129.93391
#> 18 98.64513 173.93139 190.78519 152.87092 108.20865 140.90585 99.79503
#> 19 146.76182 121.90673 199.53307 174.65382 221.52282 135.58557 145.39171
#> 20 145.44988 155.39075 127.12557 205.12120 135.80232 140.19118 105.33722
#> 21 144.22909 88.42659 133.36863 136.20200 149.97343 123.58212 149.15485
#> 22 77.50024 148.31076 112.41375 120.31431 217.21700 131.85235 105.77658
#> 23 178.62705 138.03047 151.34307 176.86262 226.36086 222.72993 166.50805
#> 24 131.33487 168.75010 144.91455 114.17635 167.56778 132.12395 163.18861
#> 25 189.00121 145.51388 89.20254 162.34954 116.20897 131.21528 137.72366
#> 26 177.19058 149.49713 121.29631 131.20777 129.08716 149.75898 188.64200
#> 27 179.53207 161.00383 192.65908 111.39228 93.78502 126.23654 141.49655
#> 28 156.85976 138.08462 135.51942 132.57034 115.48046 151.02738 100.83030
#> 29 172.00178 155.47571 134.10873 193.89878 192.63929 170.97542 127.00404
#> 30 160.03235 123.36168 151.32547 120.19444 171.84692 126.43097 153.21790
#> 31 142.73124 121.22444 137.71340 139.14134 228.70061 98.38036 173.74738
#> 32 163.69546 151.60239 139.87557 162.97546 153.64335 137.89799 96.58310
#> 33 139.91584 113.82856 144.12502 168.00912 185.06124 159.30621 114.21858
#> 34 118.60255 111.02796 135.85433 160.21549 169.25268 114.40709 177.77873
#> 35 111.53624 135.75861 137.22564 120.41312 162.96794 165.65371 132.54810
#> 36 141.88905 136.44579 116.30800 149.45404 159.58985 216.87430 115.96152
#> 37 168.42692 120.73995 141.02927 149.65292 163.17299 184.35580 123.39997
#> 38 118.12692 120.95846 106.21947 95.24047 140.10679 110.23412 111.42971
#> 39 140.75078 171.87613 105.18287 146.85064 139.77149 140.08613 156.15351
#> 40 125.16554 127.51253 171.52505 142.95273 132.89474 157.96192 169.39175
#> 41 154.43246 138.62955 148.82826 174.46699 189.99985 139.92258 128.93020
#> 42 137.18535 132.01065 141.50503 197.09304 149.51984 187.30512 148.11743
#> 43 168.72966 167.45133 148.90523 98.08387 214.86655 128.81215 131.37275
#> 44 116.53132 102.78026 166.04307 135.90853 122.39914 149.76654 116.52017
#> 45 171.40576 114.31848 140.70313 131.83608 98.81261 155.82964 144.14875
#> 46 136.38422 159.71070 182.34255 167.93693 141.47571 162.44664 162.28427
#> 47 94.23191 190.30190 131.57428 158.13349 154.46660 117.45466 98.20392
#> 48 176.27532 131.56702 175.26901 106.71867 179.41642 132.25168 157.32601
#> 49 135.02601 143.02540 146.98142 113.73427 128.40506 130.66558 133.15190
#> 50 123.37749 137.65855 137.75333 159.09431 127.63693 135.09683 212.97384
#> 51 142.53113 154.48536 125.05302 117.71794 144.40922 175.00135 122.01067
#> 52 163.33794 176.82883 140.26340 86.95519 130.57713 122.44501 125.29554
#> 53 154.75637 152.41459 124.64661 156.00459 140.06693 97.71946 162.49488
#> 54 169.65302 163.25135 174.47116 103.68960 119.29346 149.80891 172.90797
#> 55 150.91978 98.49893 119.06761 135.69739 138.82382 102.77848 176.30407
#> 56 171.19151 181.98949 152.77896 109.45666 118.89750 143.41229 115.24077
#> 57 142.15999 126.70304 127.26604 144.30520 177.03485 178.81867 151.89968
#> 58 137.75963 133.56338 162.81770 132.86220 133.74097 170.42361 72.00191
#> 59 153.15005 139.97899 139.36732 105.29047 129.23231 136.95028 152.30742
#> 60 183.50655 172.93153 119.52994 179.62976 167.32639 169.85753 126.96885
#> 61 160.04242 110.68325 144.17584 203.14916 137.93523 133.38678 116.53730
#> 62 165.29590 151.88126 141.85100 128.24976 166.67573 147.31708 205.65401
#> 63 161.49065 111.88172 127.52463 153.93291 156.35382 172.57065 118.98497
#> 64 187.29301 180.77306 135.62019 168.89627 145.81305 114.09015 119.89152
#> 65 149.59176 104.67738 152.75293 167.97606 144.72368 129.27171 154.16107
#> 66 185.93447 166.74373 130.68865 133.63313 147.38035 113.62497 107.80571
#> 67 189.44294 128.63910 138.69346 153.10409 104.27821 118.63941 120.68062
#> 68 108.93392 129.82867 114.26113 173.44618 212.11985 177.30256 150.45316
#> 69 132.43397 126.83912 158.60956 159.34707 164.56646 161.90964 192.25618
#> 70 136.17406 116.95184 133.01425 128.07568 117.15701 140.44289 147.38681
#> 71 117.98421 139.66682 149.96809 178.65193 156.34516 121.33355 148.40827
#> 72 155.87204 127.89444 163.12975 175.73652 171.29815 95.59407 121.15379
#> 73 144.74701 182.38883 155.35096 160.75360 115.05246 149.66405 145.78086
#> 74 176.70679 162.04054 152.31783 190.18228 176.50492 182.01136 135.65073
#> 75 136.10517 100.34024 141.54730 176.31093 143.00608 143.98044 154.73191
#> 76 183.05370 103.41441 137.09786 168.49059 111.52272 101.26147 148.73211
#> 77 160.39397 112.34053 157.95759 116.11384 140.97881 129.25549 104.19151
#> 78 185.48698 136.39326 178.69966 112.97186 150.31052 117.93729 118.98760
#> 79 170.18142 164.28004 86.92166 191.90845 165.69606 127.99919 155.22401
#> 80 173.46872 132.03322 144.41601 124.10896 159.94914 191.11107 109.24537
#> 81 158.66655 189.18053 157.43184 127.25322 167.27427 145.21845 137.97146
#> 82 138.64645 171.95974 164.30303 155.46261 149.96127 83.00759 105.70354
#> 83 170.82594 208.01383 125.67612 128.18215 154.66352 122.73331 144.29716
#> 84 118.25818 141.06687 120.48415 135.38601 148.08735 178.28947 157.90375
#> 85 107.22170 174.68200 139.82389 163.51852 205.32098 152.68241 136.69555
#> 86 152.74897 204.76911 136.59917 167.95307 118.09719 132.90654 128.01009
#> 87 164.70989 171.47352 171.96567 191.61977 143.02314 110.99619 136.07745
#> 88 187.90291 108.72985 127.37064 86.24131 166.04394 136.56392 108.65707
#> 89 177.35862 114.88868 127.63264 114.03414 147.90756 150.36166 114.22137
#> 90 170.24155 122.87071 144.88045 151.73199 195.34020 124.52237 166.21762
#> 91 107.20805 102.01781 184.94572 197.98942 180.34172 133.53967 138.32017
#> 92 165.06989 156.40293 127.71484 104.11640 122.38703 157.77631 142.05474
#> 93 131.57759 165.06823 149.98789 224.29848 158.85693 187.83668 170.13196
#> 94 163.52462 131.92110 149.94273 173.44589 114.66168 115.26817 132.96696
#> 95 236.74991 143.67160 162.03612 123.55417 141.65654 129.33231 157.94876
#> 96 125.31123 138.77398 126.02873 181.64131 128.49287 116.08790 99.92635
#> 97 171.05130 202.74235 126.16718 135.54263 115.79488 108.57026 134.72792
#> 98 146.13239 122.93164 163.78158 240.11379 177.62143 127.60179 174.19292
#> 99 119.90107 176.67327 125.18370 200.54795 185.44578 158.42220 85.14491
#> 100 135.94622 161.40311 170.24227 180.48176 74.89803 154.04619 156.89536
#> B.4_1
#> 1 158.95106
#> 2 127.33277
#> 3 182.26554
#> 4 138.40140
#> 5 216.51755
#> 6 161.83396
#> 7 123.86341
#> 8 114.14400
#> 9 182.42093
#> 10 119.99527
#> 11 147.64032
#> 12 137.50043
#> 13 167.73681
#> 14 173.81418
#> 15 160.67309
#> 16 168.53794
#> 17 157.21792
#> 18 144.62790
#> 19 162.39087
#> 20 179.98769
#> 21 145.71762
#> 22 133.58680
#> 23 194.42441
#> 24 146.13222
#> 25 133.56678
#> 26 125.03868
#> 27 213.18534
#> 28 123.71904
#> 29 167.38160
#> 30 129.22928
#> 31 95.34245
#> 32 146.52435
#> 33 170.99716
#> 34 167.11236
#> 35 124.54871
#> 36 143.35381
#> 37 149.94561
#> 38 173.73283
#> 39 129.32817
#> 40 119.67268
#> 41 131.94817
#> 42 143.36369
#> 43 179.79637
#> 44 181.85425
#> 45 188.49693
#> 46 168.17354
#> 47 166.69336
#> 48 179.46099
#> 49 132.49543
#> 50 153.14814
#> 51 132.83920
#> 52 133.22302
#> 53 186.27361
#> 54 162.26204
#> 55 187.39131
#> 56 152.50999
#> 57 137.66761
#> 58 167.49420
#> 59 107.58681
#> 60 156.92992
#> 61 134.35422
#> 62 113.06585
#> 63 171.76279
#> 64 153.53890
#> 65 157.63878
#> 66 134.65172
#> 67 110.97550
#> 68 121.16068
#> 69 133.36843
#> 70 151.81463
#> 71 160.27338
#> 72 150.66634
#> 73 122.86705
#> 74 119.11739
#> 75 148.76254
#> 76 163.92544
#> 77 183.84516
#> 78 150.66294
#> 79 212.21201
#> 80 173.08564
#> 81 215.85679
#> 82 137.21647
#> 83 165.78361
#> 84 166.69018
#> 85 85.58729
#> 86 152.27006
#> 87 118.98352
#> 88 179.13747
#> 89 146.58365
#> 90 111.55352
#> 91 201.46264
#> 92 152.85726
#> 93 125.30626
#> 94 103.72387
#> 95 148.60806
#> 96 167.21946
#> 97 157.32018
#> 98 214.25658
#> 99 119.25753
#> 100 161.82133