This function provides an interface to software SigProfiler.
More please see https://github.com/AlexandrovLab/SigProfilerExtractor.
Typically, a reference genome is not required because the input is a matrix (my understanding).
If you are using refitting result by SigProfiler, please make sure you have input the matrix same order as examples at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/tree/master/SigProfilerMatrixGenerator/references/matrix/BRCA_example. If not, use sigprofiler_reorder() firstly.
sigprofiler_extract(
nmf_matrix,
output,
output_matrix_only = FALSE,
range = 2:5,
nrun = 10L,
refit = FALSE,
refit_plot = FALSE,
is_exome = FALSE,
init_method = c("random", "nndsvd_min", "nndsvd", "nndsvda", "nndsvdar"),
cores = -1L,
genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
use_conda = FALSE,
py_path = NULL,
sigprofiler_version = "1.1.3"
)
sigprofiler_import(
output,
order_by_expo = FALSE,
type = c("suggest", "refit", "all")
)
sigprofiler_reorder(
nmf_matrix,
type = c("SBS96", "SBS6", "SBS12", "SBS192", "SBS1536", "SBS3072", "DBS78", "DBS312",
"DBS1248", "DBS4992")
)a matrix used for NMF decomposition with rows indicate samples and columns indicate components.
output directory.
if TRUE, only generate matrix file for SigProfiler
so user can call SigProfiler with the input by himself.
signature number range, i.e. 2:5.
the number of iteration to be performed to extract each signature number.
if TRUE, then refit the denovo signatures with nnls. Same
meaning as optimize option in sig_extract or sig_auto_extract.
if TRUE, SigProfiler will make
denovo to COSMIC sigantures decompostion plots. However, this may fail due
to some matrix cannot be identified by SigProfiler plot program.
if TRUE, the exomes will be extracted.
the initialization algorithm for W and H matrix of NMF. Options are 'random', 'nndsvd', 'nndsvda', 'nndsvdar', 'alexandrov-lab-custom' and 'nndsvd_min'.
number of cores used for computation.
I think this option is useless when input is matrix, keep it
in case it is useful.
if TRUE, create an independent conda environment to run SigProfiler.
path to Python executable file, e.g. '/Users/wsx/anaconda3/bin/python'.
version of SigProfilerExtractor. If this
package is not installed, the specified package will be installed.
If this package is installed, this option is useless.
if TRUE, order the import signatures by their exposures, e.g. the signature
contributed the most exposure in all samples will be named as Sig1.
mutational signature type.
For sigprofiler_extract(), returns nothing. See output directory.
For sigprofiler_import(), a list containing Signature object.
A NMF matrix for input of sigprofiler_extract().
if (FALSE) {
load(system.file("extdata", "toy_copynumber_tally_W.RData",
package = "sigminer", mustWork = TRUE
))
reticulate::conda_list()
sigprofiler_extract(cn_tally_W$nmf_matrix, "~/test/test_sigminer",
use_conda = TRUE
)
sigprofiler_extract(cn_tally_W$nmf_matrix, "~/test/test_sigminer",
use_conda = FALSE, py_path = "/Users/wsx/anaconda3/bin/python"
)
}
data("simulated_catalogs")
sigprofiler_reorder(t(simulated_catalogs$set1))
#> Downloading reference file...
#> Reordering...
#> Done
#> A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T
#> Sample_1 911 761 88 744 487 248 80 472
#> Sample_2 195 175 19 174 70 33 3 72
#> Sample_3 95 51 12 55 54 32 9 57
#> Sample_4 131 71 14 77 85 43 16 85
#> Sample_5 33 10 2 14 8 4 2 10
#> Sample_6 30 18 2 19 10 6 2 11
#> Sample_7 28 9 2 13 7 5 2 8
#> Sample_8 48 23 4 23 11 9 4 14
#> Sample_9 70 48 7 57 71 40 13 68
#> Sample_10 227 153 19 160 99 57 20 101
#> Sample_11 47 32 7 29 33 21 6 35
#> Sample_12 1077 520 94 584 531 291 127 538
#> Sample_13 37 21 3 24 9 4 1 9
#> Sample_14 26 16 4 16 20 11 3 20
#> Sample_15 119 57 13 69 70 42 13 73
#> Sample_16 214 76 15 100 58 34 18 63
#> Sample_17 184 140 32 115 57 46 5 63
#> Sample_18 93 81 7 87 26 15 2 26
#> Sample_19 653 255 60 310 173 119 46 193
#> Sample_20 59 20 5 26 8 7 3 10
#> Sample_21 288 250 23 245 161 81 27 160
#> Sample_22 600 431 76 400 474 279 99 477
#> Sample_23 127 43 7 62 17 14 7 22
#> Sample_24 779 435 76 467 511 281 108 517
#> Sample_25 221 61 12 96 15 19 11 26
#> Sample_26 56 52 6 49 17 12 1 20
#> Sample_27 158 109 15 115 57 29 7 58
#> Sample_28 86 29 6 39 22 15 7 24
#> Sample_29 55 45 5 46 18 11 2 18
#> Sample_30 42 36 4 37 12 7 1 12
#> A[C>T]A A[C>T]C A[C>T]G A[C>T]T A[T>A]A A[T>A]C A[T>A]G A[T>A]T
#> Sample_1 675 282 349 586 381 365 358 534
#> Sample_2 248 103 389 171 85 91 79 147
#> Sample_3 194 103 372 113 41 45 44 64
#> Sample_4 109 54 48 76 52 47 49 56
#> Sample_5 13 5 9 9 4 3 4 4
#> Sample_6 25 12 42 18 7 7 7 11
#> Sample_7 20 10 35 13 5 5 6 7
#> Sample_8 48 24 220 25 10 6 9 16
#> Sample_9 104 52 73 74 31 32 33 41
#> Sample_10 160 77 123 140 79 68 90 115
#> Sample_11 103 55 251 62 26 23 30 38
#> Sample_12 632 322 284 490 305 263 301 324
#> Sample_13 19 8 21 16 11 10 10 16
#> Sample_14 51 25 39 31 17 16 18 20
#> Sample_15 138 75 186 96 50 42 60 64
#> Sample_16 73 37 42 61 39 31 39 39
#> Sample_17 560 270 1928 266 97 106 73 161
#> Sample_18 76 28 141 66 34 34 36 64
#> Sample_19 481 255 1004 320 181 146 201 222
#> Sample_20 33 17 78 21 12 10 13 14
#> Sample_21 205 85 186 187 112 103 109 171
#> Sample_22 869 466 1702 590 289 244 320 382
#> Sample_23 56 29 98 45 19 15 24 28
#> Sample_24 630 339 406 495 289 237 320 340
#> Sample_25 125 62 409 75 20 15 25 34
#> Sample_26 138 66 449 77 21 26 18 50
#> Sample_27 114 49 79 93 65 60 64 91
#> Sample_28 39 22 32 32 18 14 22 21
#> Sample_29 59 25 135 42 22 22 22 37
#> Sample_30 53 23 84 37 18 20 17 32
#> A[T>C]A A[T>C]C A[T>C]G A[T>C]T A[T>G]A A[T>G]C A[T>G]G A[T>G]T
#> Sample_1 1085 704 1014 896 107 51 245 206
#> Sample_2 250 155 270 189 24 13 39 33
#> Sample_3 190 98 219 124 13 15 23 26
#> Sample_4 211 125 202 148 15 11 32 28
#> Sample_5 5 3 4 7 1 1 3 2
#> Sample_6 12 7 15 13 2 2 5 4
#> Sample_7 16 8 18 13 2 3 4 7
#> Sample_8 27 13 21 22 3 4 6 7
#> Sample_9 83 69 79 81 9 33 39 146
#> Sample_10 184 82 142 180 26 13 52 32
#> Sample_11 102 42 91 75 10 8 15 14
#> Sample_12 1073 659 1034 831 82 65 229 180
#> Sample_13 34 21 33 25 3 2 5 3
#> Sample_14 89 48 84 58 5 4 8 8
#> Sample_15 177 81 146 140 18 23 34 71
#> Sample_16 132 85 132 103 9 9 28 20
#> Sample_17 636 419 699 353 26 46 40 130
#> Sample_18 49 37 36 61 11 16 23 71
#> Sample_19 815 432 747 560 56 49 95 80
#> Sample_20 60 37 59 39 3 4 6 11
#> Sample_21 166 91 133 201 34 13 76 49
#> Sample_22 925 412 783 769 102 73 207 170
#> Sample_23 45 26 48 44 5 10 14 29
#> Sample_24 812 359 665 718 97 64 208 146
#> Sample_25 48 43 64 47 4 27 22 92
#> Sample_26 53 34 80 41 6 11 13 32
#> Sample_27 225 129 205 164 19 9 30 22
#> Sample_28 66 32 58 52 6 5 12 8
#> Sample_29 69 48 64 54 7 10 14 41
#> Sample_30 67 45 74 47 5 5 10 18
#> C[C>A]A C[C>A]C C[C>A]G C[C>A]T C[C>G]A C[C>G]C C[C>G]G C[C>G]T
#> Sample_1 883 725 84 696 349 295 66 462
#> Sample_2 225 230 44 337 61 38 4 72
#> Sample_3 142 127 55 266 39 30 12 52
#> Sample_4 170 88 32 101 67 48 18 91
#> Sample_5 55 15 10 25 8 5 4 13
#> Sample_6 41 25 9 42 7 7 3 11
#> Sample_7 45 17 11 35 5 5 3 8
#> Sample_8 60 25 11 34 8 8 5 13
#> Sample_9 55 41 9 48 54 39 12 67
#> Sample_10 229 125 32 169 68 66 22 94
#> Sample_11 37 35 14 71 23 19 7 29
#> Sample_12 1464 645 265 795 370 332 141 554
#> Sample_13 53 27 9 35 8 6 2 11
#> Sample_14 28 22 8 30 15 11 3 18
#> Sample_15 128 48 29 89 56 42 18 71
#> Sample_16 336 114 63 159 40 41 25 69
#> Sample_17 247 298 82 420 34 27 4 34
#> Sample_18 79 63 4 70 23 16 2 24
#> Sample_19 925 334 188 494 115 127 71 177
#> Sample_20 94 32 19 45 5 7 6 10
#> Sample_21 255 216 23 255 123 95 23 164
#> Sample_22 453 366 100 551 319 285 94 426
#> Sample_23 200 69 42 127 11 16 13 22
#> Sample_24 847 386 158 574 376 308 119 520
#> Sample_25 370 119 79 221 9 17 22 27
#> Sample_26 68 98 26 187 13 8 1 15
#> Sample_27 184 112 26 128 47 35 10 59
#> Sample_28 127 38 25 64 14 17 10 24
#> Sample_29 50 42 5 41 14 11 2 16
#> Sample_30 49 50 10 71 8 8 1 9
#> C[C>T]A C[C>T]C C[C>T]G C[C>T]T C[T>A]A C[T>A]C C[T>A]G C[T>A]T
#> Sample_1 556 312 245 783 290 550 427 683
#> Sample_2 175 95 352 209 61 117 87 138
#> Sample_3 136 105 365 121 19 40 43 42
#> Sample_4 135 78 55 124 28 59 52 63
#> Sample_5 26 9 15 14 2 4 5 5
#> Sample_6 18 10 42 18 5 10 9 13
#> Sample_7 19 12 37 13 2 6 7 10
#> Sample_8 41 31 130 33 4 8 9 10
#> Sample_9 148 56 84 98 21 75 54 173
#> Sample_10 140 92 92 158 59 88 100 128
#> Sample_11 90 67 176 75 13 18 27 26
#> Sample_12 738 437 371 711 182 380 352 431
#> Sample_13 19 10 20 22 7 14 11 16
#> Sample_14 65 35 39 55 8 17 15 17
#> Sample_15 169 103 142 124 25 49 62 100
#> Sample_16 100 56 69 89 19 48 46 52
#> Sample_17 481 315 1331 433 28 137 57 138
#> Sample_18 69 26 90 72 28 63 47 124
#> Sample_19 557 380 712 487 74 160 182 178
#> Sample_20 43 26 59 37 4 14 12 17
#> Sample_21 116 77 127 183 96 149 138 207
#> Sample_22 736 566 1120 692 185 271 335 380
#> Sample_23 58 34 108 45 9 26 29 47
#> Sample_24 654 448 358 583 184 272 352 384
#> Sample_25 151 74 341 90 4 43 37 101
#> Sample_26 65 53 355 67 14 34 23 51
#> Sample_27 115 68 62 135 40 75 65 90
#> Sample_28 49 33 37 41 9 16 23 21
#> Sample_29 58 29 85 59 15 39 26 67
#> Sample_30 36 21 78 47 12 30 20 40
#> C[T>C]A C[T>C]C C[T>C]G C[T>C]T C[T>G]A C[T>G]C C[T>G]G C[T>G]T
#> Sample_1 643 944 828 875 79 197 310 498
#> Sample_2 144 185 243 164 16 38 60 71
#> Sample_3 100 97 198 107 8 32 48 75
#> Sample_4 121 151 159 140 10 31 47 55
#> Sample_5 2 5 3 5 0 2 5 7
#> Sample_6 6 9 14 8 1 4 8 7
#> Sample_7 8 13 19 25 1 6 8 50
#> Sample_8 9 14 15 15 1 6 9 8
#> Sample_9 65 208 160 468 7 98 85 1112
#> Sample_10 74 95 93 112 16 28 62 67
#> Sample_11 42 37 68 53 5 13 22 36
#> Sample_12 621 835 816 744 62 200 327 323
#> Sample_13 19 26 27 23 2 5 8 7
#> Sample_14 49 53 67 55 4 10 14 21
#> Sample_15 80 128 139 259 10 52 60 488
#> Sample_16 78 111 107 92 7 27 45 38
#> Sample_17 399 531 671 594 17 124 110 617
#> Sample_18 29 108 74 234 6 46 43 541
#> Sample_19 413 480 571 491 33 99 157 198
#> Sample_20 35 50 53 56 2 11 14 58
#> Sample_21 73 126 95 121 22 40 85 76
#> Sample_22 395 429 554 540 62 147 264 346
#> Sample_23 22 51 58 96 3 24 31 208
#> Sample_24 345 397 444 483 60 135 267 318
#> Sample_25 34 130 127 291 1 68 65 721
#> Sample_26 30 51 101 88 3 27 30 185
#> Sample_27 121 154 160 146 12 25 42 49
#> Sample_28 30 36 43 39 3 10 19 21
#> Sample_29 43 91 76 152 4 29 27 289
#> Sample_30 43 65 75 80 4 16 18 107
#> G[C>A]A G[C>A]C G[C>A]G G[C>A]T G[C>G]A G[C>G]C G[C>G]G G[C>G]T
#> Sample_1 548 445 47 493 232 192 27 337
#> Sample_2 133 110 16 132 27 30 2 47
#> Sample_3 137 67 24 114 23 31 4 33
#> Sample_4 169 66 19 112 39 33 6 55
#> Sample_5 74 12 6 43 4 3 1 6
#> Sample_6 44 14 4 31 5 5 1 8
#> Sample_7 61 12 6 38 3 3 1 5
#> Sample_8 80 19 6 47 5 7 1 8
#> Sample_9 61 39 11 50 36 28 5 52
#> Sample_10 241 103 22 177 47 41 8 64
#> Sample_11 37 31 9 34 15 17 3 18
#> Sample_12 1651 476 150 1048 257 217 40 362
#> Sample_13 57 16 5 36 4 3 0 6
#> Sample_14 20 18 5 16 9 8 1 10
#> Sample_15 175 63 23 115 33 29 6 41
#> Sample_16 430 82 34 252 28 23 5 40
#> Sample_17 157 137 34 114 20 47 0 29
#> Sample_18 71 42 5 57 12 9 1 19
#> Sample_19 1201 290 115 704 80 81 16 90
#> Sample_20 125 24 11 70 4 4 1 4
#> Sample_21 169 137 12 171 76 64 10 116
#> Sample_22 397 343 72 378 227 222 37 301
#> Sample_23 276 49 23 164 8 9 2 12
#> Sample_24 966 379 108 688 243 211 41 331
#> Sample_25 534 81 43 305 8 10 2 14
#> Sample_26 44 39 8 51 6 14 0 14
#> Sample_27 170 77 17 117 25 21 3 33
#> Sample_28 172 35 15 102 11 10 2 13
#> Sample_29 42 27 4 31 9 8 1 12
#> Sample_30 31 24 4 28 5 6 0 8
#> G[C>T]A G[C>T]C G[C>T]G G[C>T]T G[T>A]A G[T>A]C G[T>A]G G[T>A]T
#> Sample_1 439 275 221 403 192 243 263 407
#> Sample_2 290 298 496 248 42 58 49 96
#> Sample_3 309 340 518 258 24 28 27 29
#> Sample_4 108 82 53 90 25 29 33 36
#> Sample_5 13 8 11 7 2 2 2 4
#> Sample_6 32 32 54 25 4 5 5 9
#> Sample_7 27 29 47 22 3 3 4 5
#> Sample_8 41 40 136 29 4 4 5 8
#> Sample_9 72 48 63 54 17 27 39 39
#> Sample_10 109 84 88 104 52 44 60 79
#> Sample_11 118 120 212 99 17 12 18 15
#> Sample_12 590 424 276 474 155 183 215 250
#> Sample_13 16 16 25 15 5 6 6 11
#> Sample_14 55 46 41 46 9 9 10 9
#> Sample_15 119 108 145 106 33 25 39 34
#> Sample_16 68 52 50 53 19 23 24 34
#> Sample_17 681 714 1573 537 21 64 39 67
#> Sample_18 24 18 90 26 19 24 29 50
#> Sample_19 440 415 707 387 98 87 102 114
#> Sample_20 29 27 55 24 5 7 6 9
#> Sample_21 145 115 173 130 64 68 84 130
#> Sample_22 856 783 1260 718 182 146 224 211
#> Sample_23 62 69 123 53 12 13 15 22
#> Sample_24 575 462 361 497 186 147 222 216
#> Sample_25 131 144 364 97 8 17 18 30
#> Sample_26 202 234 479 163 9 18 14 29
#> Sample_27 81 67 69 82 34 36 37 58
#> Sample_28 35 32 31 32 12 9 12 13
#> Sample_29 33 28 84 30 10 15 16 27
#> Sample_30 59 63 106 53 9 14 12 22
#> G[T>C]A G[T>C]C G[T>C]G G[T>C]T G[T>G]A G[T>G]C G[T>G]G G[T>G]T
#> Sample_1 1015 567 759 820 70 82 326 270
#> Sample_2 251 132 192 185 5 9 34 46
#> Sample_3 158 83 133 112 6 7 30 28
#> Sample_4 196 104 151 154 11 10 50 29
#> Sample_5 2 3 5 5 1 1 8 4
#> Sample_6 8 6 9 7 2 2 9 5
#> Sample_7 10 8 11 10 1 2 7 14
#> Sample_8 18 13 12 20 2 2 12 5
#> Sample_9 36 65 50 69 10 47 59 280
#> Sample_10 80 57 75 91 16 9 70 39
#> Sample_11 57 33 46 50 4 2 16 11
#> Sample_12 958 539 777 793 91 79 415 205
#> Sample_13 34 18 27 27 1 1 7 5
#> Sample_14 78 39 59 60 2 1 8 8
#> Sample_15 84 67 81 96 9 17 44 123
#> Sample_16 128 73 111 110 12 9 62 28
#> Sample_17 739 386 526 539 1 31 35 175
#> Sample_18 19 35 24 41 2 20 24 141
#> Sample_19 677 365 538 567 27 8 149 85
#> Sample_20 61 34 49 50 2 2 12 18
#> Sample_21 80 64 70 89 23 23 104 61
#> Sample_22 485 307 393 459 72 55 285 148
#> Sample_23 23 24 34 33 4 8 30 58
#> Sample_24 386 259 359 400 78 52 324 150
#> Sample_25 32 51 55 61 6 26 54 186
#> Sample_26 51 34 44 37 1 10 13 53
#> Sample_27 203 106 154 162 6 3 32 28
#> Sample_28 43 26 40 41 4 1 22 10
#> Sample_29 62 44 49 59 2 11 16 77
#> Sample_30 71 39 55 54 1 5 9 32
#> T[C>A]A T[C>A]C T[C>A]G T[C>A]T T[C>G]A T[C>G]C T[C>G]G T[C>G]T
#> Sample_1 621 617 71 813 310 367 35 555
#> Sample_2 424 224 33 332 1479 329 51 1822
#> Sample_3 223 129 34 206 710 193 29 847
#> Sample_4 296 175 36 244 1051 293 42 1266
#> Sample_5 103 50 13 100 326 73 13 409
#> Sample_6 35 24 6 53 23 9 2 42
#> Sample_7 54 30 9 67 114 32 5 136
#> Sample_8 58 43 12 88 17 13 2 32
#> Sample_9 83 65 18 89 235 97 13 318
#> Sample_10 221 161 37 314 95 75 12 180
#> Sample_11 92 57 15 82 240 68 12 307
#> Sample_12 1269 979 239 1748 1504 759 105 2013
#> Sample_13 73 40 9 73 207 52 7 245
#> Sample_14 80 45 10 55 279 64 11 357
#> Sample_15 289 154 42 257 929 253 39 1117
#> Sample_16 278 192 56 421 234 111 16 302
#> Sample_17 216 226 52 244 126 47 6 200
#> Sample_18 103 61 11 118 190 50 6 236
#> Sample_19 903 620 188 1252 817 343 52 1003
#> Sample_20 73 53 17 118 5 12 2 8
#> Sample_21 329 218 24 327 869 286 38 1091
#> Sample_22 498 482 107 646 220 362 52 465
#> Sample_23 155 101 35 266 7 23 4 17
#> Sample_24 1312 812 188 1329 3550 1145 170 4391
#> Sample_25 302 193 71 515 51 36 8 98
#> Sample_26 77 50 10 86 183 47 6 220
#> Sample_27 284 163 31 255 837 219 31 992
#> Sample_28 103 72 24 168 10 24 4 20
#> Sample_29 43 37 7 58 11 12 1 19
#> Sample_30 33 28 5 45 6 6 0 8
#> T[C>T]A T[C>T]C T[C>T]G T[C>T]T T[T>A]A T[T>A]C T[T>A]G T[T>A]T
#> Sample_1 435 394 129 454 385 483 257 714
#> Sample_2 2045 415 339 997 88 101 50 156
#> Sample_3 368 141 181 136 40 42 28 47
#> Sample_4 494 147 51 168 49 68 36 71
#> Sample_5 525 101 59 251 4 4 2 4
#> Sample_6 199 47 40 112 7 7 5 12
#> Sample_7 60 22 23 22 6 4 3 6
#> Sample_8 130 53 113 79 12 7 5 12
#> Sample_9 179 133 87 137 29 37 22 57
#> Sample_10 640 219 117 395 85 70 57 130
#> Sample_11 391 131 144 207 27 19 18 28
#> Sample_12 1027 643 237 533 298 389 222 452
#> Sample_13 99 22 15 33 11 14 6 18
#> Sample_14 592 138 74 302 16 22 12 21
#> Sample_15 468 188 129 190 51 41 36 58
#> Sample_16 170 89 47 75 41 51 27 55
#> Sample_17 1286 496 978 788 107 160 47 140
#> Sample_18 204 76 92 135 39 34 20 73
#> Sample_19 704 480 523 369 201 205 123 219
#> Sample_20 37 32 44 25 14 17 8 16
#> Sample_21 402 137 84 193 113 106 75 207
#> Sample_22 413 661 753 434 293 242 213 384
#> Sample_23 56 53 65 41 23 17 13 27
#> Sample_24 1721 742 289 690 281 249 216 376
#> Sample_25 583 205 293 345 28 21 10 28
#> Sample_26 124 60 204 69 23 19 10 37
#> Sample_27 412 117 52 155 67 78 42 105
#> Sample_28 38 43 24 26 20 18 14 22
#> Sample_29 46 43 70 51 25 28 13 44
#> Sample_30 31 24 38 30 20 25 11 36
#> T[T>C]A T[T>C]C T[T>C]G T[T>C]T T[T>G]A T[T>G]C T[T>G]G T[T>G]T
#> Sample_1 928 744 583 834 126 166 252 405
#> Sample_2 203 149 143 174 19 27 34 69
#> Sample_3 130 98 111 106 23 28 24 65
#> Sample_4 180 140 118 148 25 30 33 57
#> Sample_5 2 6 2 3 1 3 2 8
#> Sample_6 6 8 6 7 2 4 5 12
#> Sample_7 8 10 9 9 2 5 3 15
#> Sample_8 15 14 14 14 4 6 7 14
#> Sample_9 47 85 53 73 18 58 48 296
#> Sample_10 84 87 58 102 30 36 53 87
#> Sample_11 52 40 44 49 15 15 17 34
#> Sample_12 903 771 606 776 148 202 239 349
#> Sample_13 29 23 19 25 2 4 4 8
#> Sample_14 70 51 48 58 8 9 8 18
#> Sample_15 87 91 73 96 26 43 37 151
#> Sample_16 117 108 80 99 15 27 25 52
#> Sample_17 610 428 460 460 36 66 43 204
#> Sample_18 19 39 20 41 5 26 24 147
#> Sample_19 611 486 431 510 76 105 85 187
#> Sample_20 53 44 38 43 4 9 5 23
#> Sample_21 80 89 50 109 37 44 81 124
#> Sample_22 486 422 381 492 164 172 242 457
#> Sample_23 20 35 24 27 5 19 12 58
#> Sample_24 417 405 300 442 157 176 230 396
#> Sample_25 24 65 46 37 4 42 19 146
#> Sample_26 31 27 42 29 6 15 14 68
#> Sample_27 181 136 114 155 19 24 26 48
#> Sample_28 41 39 30 38 8 12 11 25
#> Sample_29 55 51 41 54 5 17 15 64
#> Sample_30 59 46 43 51 4 10 9 37