tests/testthat/_snaps/bagel_classifications.md
In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses
can add bagel_classification
Code
add_bagel_classifications(data = test_count_matrix, gene_column = 2, ess = ess,
noness = noness)
Output
sgRNA gene T0_- T3_A T3_B T3_C T18_A T18_B
2007 PPA1_TTTAGACTTGGGAAGACCCA PPA1 277 92 64 67 10 27
2008 PPA1_GTTGCATGAAGACATACCTG PPA1 267 143 108 46 62 2
2009 PPA1_TGGTAGTTGAAGTACCACGC PPA1 98 45 85 60 72 75
2010 PPA1_TATGAGCGGCTTCAGCACCG PPA1 388 261 179 159 20 0
3396 CCDC84_AAGAAGGTCTGGCGGCACAG CCDC84 321 238 108 181 0 9
3397 CCDC84_GTGCGGGAACACCTGAGCCA CCDC84 321 114 70 66 8 31
3398 CCDC84_CTGGTGGGAGAACAAAGCTG CCDC84 440 236 107 164 31 51
3399 CCDC84_GGAATCCAAACCTTTCACCA CCDC84 116 83 83 111 55 52
3464 MFRP_AGACGAAGACCACCAGGAGG MFRP 214 38 30 76 61 75
3465 MFRP_GGGACAGAGGGACCTACCTG MFRP 285 115 106 147 129 95
3466 MFRP_CATAGCCCACTGCCTGCCGG MFRP 618 492 312 352 398 287
3467 MFRP_GGAGGCAACAGAATCGAGCA MFRP 166 72 60 51 280 78
3599 OR10S1_GTTGCGCATCCGCACAGCCC OR10S1 185 122 104 134 268 164
3600 OR10S1_AGACAAACAGGCATCCAGGA OR10S1 526 218 165 143 377 326
3601 OR10S1_AGTGGTACATGGGTAAGCTG OR10S1 178 206 153 150 218 162
3602 OR10S1_TGAGAAGATGACCATGACAA OR10S1 592 197 187 176 209 404
3655 PANX3_CCAGACGCAGTCCTTTGAGG PANX3 528 233 173 204 250 233
3656 PANX3_CCAGCAGGAGCTGTCCACGT PANX3 698 321 225 250 317 239
3657 PANX3_TGAACAGCAGATCGGAGCTG PANX3 373 329 140 193 444 206
3658 PANX3_AAGGTATAGGTAAGTGGCGG PANX3 276 378 275 409 111 338
3951 COPB1_AGAAGGAATCCTCTCAAGGG COPB1 164 18 31 23 20 12
3952 COPB1_TATTGTGCTAGGATTTACCG COPB1 317 24 35 15 20 41
3953 COPB1_AGAAGGATGCAAGTTGCAAA COPB1 140 58 63 89 66 122
3954 COPB1_ATAACCAGAAACCATGACGG COPB1 416 49 40 24 13 39
6674 OR10A2_GACATTTCTAACCATCTACC OR10A2 195 71 69 56 93 173
6675 OR10A2_CATCTACCTGGTCACCCTGA OR10A2 544 265 265 286 326 440
6676 OR10A2_CATCAGGGTGACCAGGTAGA OR10A2 829 387 328 320 402 636
6677 OR10A2_GATGAGGCAGTTTCCCATCA OR10A2 206 103 100 111 93 296
11161 UBE2N_TTCTGTCTACAGCTAGAGCA UBE2N 342 235 136 203 314 90
11162 UBE2N_AGATACCTGTTTCTATGGCT UBE2N 221 215 171 189 80 84
12503 WDR25_ACAGCGGCAGGCATTAAGCA WDR25 583 183 115 159 20 56
12504 WDR25_CGAAGTCAAAGCCACCACTG WDR25 1182 335 246 207 27 34
12505 WDR25_GGAACTCGGAGCCTTCCCGG WDR25 83 63 63 77 1 65
12506 WDR25_CATCCGGTAGGGCCACACAG WDR25 527 262 174 199 161 75
13759 ACTR10_ACTACCATGCCGCTCTACGA ACTR10 320 86 40 123 0 18
13760 ACTR10_ATTCGATAATCACAACTCGG ACTR10 182 54 15 32 6 16
13761 ACTR10_ATATCCACAATCTAGGACCA ACTR10 353 72 53 57 35 1
13762 ACTR10_ACAGAGCCTTCCCTCAGTGA ACTR10 424 127 146 152 47 102
15352 HYPK_AAGCCACGGAAACATGACAG HYPK 276 43 43 90 8 21
15353 HYPK_GAAACATGACAGCGGTGCGG HYPK 291 120 109 150 128 34
15354 HYPK_GCGGGTCACCGACTATGCAG HYPK 192 43 31 6 0 0
15355 HYPK_GCGGGAACACATGGGCAACG HYPK 314 150 75 82 21 17
17223 PDILT_ATGACTCCAAACGTTAGCTC PDILT 199 99 58 27 116 91
17224 PDILT_GAAGAAGCCAACGATGACCA PDILT 310 200 132 150 239 236
17225 PDILT_AGTGGACATTACCATAGAGA PDILT 119 48 38 36 49 29
17228 PDILT_CAAGCCTGTGCACATCCTGG PDILT 518 286 203 240 145 166
27722 ERCC2_ATCCAGGTTGTAGATGCCAG ERCC2 491 360 205 250 182 222
27723 ERCC2_AAGGAACAGGTGCTCACCTC ERCC2 426 98 85 54 13 3
27724 ERCC2_TTATCGGCAGGCATATCCGC ERCC2 532 151 101 115 30 4
27725 ERCC2_GCGGGAGCTCAAACGCACGC ERCC2 280 94 58 66 52 5
27770 SNRPD2_TCTCCAAGATGTTCCTGCGC SNRPD2 2 2 8 19 0 0
27771 SNRPD2_CATGGTGCTGGAGAACGTGA SNRPD2 215 25 12 18 58 8
27772 SNRPD2_ACCCAGCACTCACCTATCGA SNRPD2 208 39 24 31 56 112
27773 SNRPD2_GAGGAGGAGGAATTTAACAC SNRPD2 257 33 22 45 35 35
28014 CRX_TAGGAATCTGAGATGCCCAG CRX 90 183 128 161 247 72
28015 CRX_GCTCGGAGACCCATAGGCGG CRX 330 253 217 301 279 202
28016 CRX_GGCCAGGGAAGGTCCCACGG CRX 245 127 87 137 42 85
28017 CRX_GAAATTCACCTACAATCCCA CRX 137 30 18 30 49 36
28118 RPL18_TCGAGCGTGCCAGAGGCCGA RPL18 523 68 60 74 47 49
28119 RPL18_CCTTCCCTAGGTCCTCGCAA RPL18 241 36 39 30 2 34
28120 RPL18_CAGCCGCATCCTCAGGGCAG RPL18 458 82 50 58 12 18
28121 RPL18_AGTGGACATCCGCCATAACA RPL18 298 95 49 79 74 52
30909 GJA8_TGGGCGACTGGAGTTTCCTG GJA8 523 250 117 178 267 260
30910 GJA8_AGAGGAGGGAGCCGAACCCG GJA8 308 239 109 149 187 61
30911 GJA8_AGCAGAGAGGCTGACCACGG GJA8 408 162 188 176 137 193
30912 GJA8_GGAGAAGGTGGCCGTGCCAG GJA8 315 181 144 188 249 162
32765 NPHS2_GCAAAGACAAGCCAAAGTGC NPHS2 354 128 121 174 300 264
32766 NPHS2_CAGGAAGCAGATGTCCCAGT NPHS2 538 273 206 235 542 404
32767 NPHS2_GAGGACAAGAAGCCACTCAC NPHS2 185 91 93 82 172 107
32768 NPHS2_GTTGGAGAGCGAGCGGCCCG NPHS2 174 205 115 126 248 69
33931 CELA3A_GAGGGATCTGACCTACCAGG CELA3A 133 166 140 156 79 171
33932 CELA3A_TGAGTACAACCTTGCTGTGA CELA3A 476 414 285 296 500 351
33933 CELA3A_GCAGTGCTTATAGTCCACCA CELA3A 423 215 146 199 321 259
36313 CDCP2_CAGACCGCAGCACCACCCGC CDCP2 530 396 209 183 360 298
36314 CDCP2_GGTGTTCGTGGACTTCCAGG CDCP2 128 220 125 128 141 52
36315 CDCP2_ATGGAAGGTGAGCAGCACCG CDCP2 155 143 127 145 119 131
36316 CDCP2_AGGGCTCCAGGCCCAAGCCA CDCP2 459 99 90 105 250 169
37544 CST8_GGACCATGCCCAGGTGCCGG CST8 179 110 52 43 144 36
37545 CST8_CCACAGACACTGCTTCACGT CST8 915 249 252 297 283 348
37546 CST8_AAGGCTTTCTGCAATCGCTG CST8 276 202 118 147 80 231
37547 CST8_GAATGGTGAATTCACTGTGA CST8 132 147 66 60 51 265
37648 NOP56_GCTGGCGCTGAAGGAAGTGG NOP56 294 108 44 75 76 51
37649 NOP56_AATGCCAACGCCGTGTCTGA NOP56 528 147 95 190 28 64
37650 NOP56_GATTGGTGCCGCAATACAGG NOP56 181 70 35 82 23 4
37651 NOP56_CAGCTTGTAAAGCACAGCTG NOP56 167 60 8 24 48 1
37708 DEFB123_GCACAGTCAAAGTCAGCAAA DEFB123 492 141 103 76 179 270
37709 DEFB123_CAGGTGGCACCCAAAGATGC DEFB123 556 264 143 118 247 249
37710 DEFB123_CCGTTACAGATGCTCCAAGA DEFB123 493 151 94 90 180 121
37711 DEFB123_AATGGCCACCACCTTTCTTT DEFB123 644 333 157 207 379 209
47639 GFM1_TTAATTGGAAGGCCTGCCGA GFM1 435 258 159 155 143 22
47640 GFM1_AATGGGCTCCAACCCAGCCA GFM1 509 136 78 110 109 110
47641 GFM1_AGCGTTTATGCAGATACCCA GFM1 166 111 98 111 16 44
47642 GFM1_ATTCAATTAGCTCCTGCCGG GFM1 664 265 246 240 32 30
48225 TMEM207_TGAAGGTGAATTCCAACAGT TMEM207 572 196 115 202 404 239
48226 TMEM207_TGATTCTCACAGGCGCACCA TMEM207 264 103 107 112 149 160
48227 TMEM207_TTGGTGGCAGCTCTTCTCTG TMEM207 404 381 228 324 275 205
48228 TMEM207_ATGACCAACACCCTAATGGC TMEM207 325 197 175 130 99 177
48401 NCBP2_ACTGGCACAGAACCAGTGAG NCBP2 299 130 60 87 128 231
48402 NCBP2_GAGGGCAGGCAATACGGCCG NCBP2 244 99 71 77 141 69
48403 NCBP2_GTACTGGCTCAGCTCCACGT NCBP2 449 51 53 82 22 0
48404 NCBP2_GCTGCGCAGCGACTCCTACG NCBP2 397 36 50 58 0 0
53441 IL9_TGTGCTCCGTGGCAGGCCAG IL9 504 346 184 242 329 219
53442 IL9_TGCCACGGAGCACAGGAGCA IL9 649 312 133 196 497 214
53443 IL9_CAGGGCAGAGGTAAGGACCA IL9 834 225 166 211 376 156
53444 IL9_TGTCAAGATGCTTCTGGCCA IL9 725 361 308 379 793 569
58856 BYSL_TCGCGGGACAGGAGAAGCGG BYSL 682 129 79 71 33 46
58857 BYSL_GGAGTGGCCCACCCTGGAGA BYSL 332 83 72 73 149 31
58858 BYSL_GGTCCTAGAAGTGTACAGGG BYSL 340 139 88 96 24 18
58859 BYSL_GTATTATCTAAGTACCGCAG BYSL 31 13 20 34 1 15
59238 MCM3_TCAGCCCTCTTTCTCTGCTG MCM3 481 196 161 226 182 294
59239 MCM3_AAGAAGGGAGGCTACACCTC MCM3 108 74 86 90 68 32
59240 MCM3_GGTAGGATAGACAGAGCTGG MCM3 220 110 80 76 71 68
59241 MCM3_GAAGGCAACCAGCTCCTCAA MCM3 185 52 46 79 49 34
62425 RFC2_TGTACCGGAGGACTGCACAG RFC2 409 34 19 27 0 0
62426 RFC2_TTTCTTCTCAGCATGACCGA RFC2 420 157 68 127 102 117
62427 RFC2_TGTGCCCAACATCATCATTG RFC2 615 134 89 110 77 91
62428 RFC2_GAGGTGGAGGCCGTCTGTGG RFC2 440 93 52 61 27 10
66194 RPL12_TCTTCTGCAGTTAAACACAG RPL12 208 6 15 9 78 79
66195 RPL12_GGGATAACGTACCAGACCCA RPL12 218 11 2 5 1 0
66196 RPL12_GGATAACGTACCAGACCCAG RPL12 329 5 20 19 7 22
66197 RPL12_GATAACGTACCAGACCCAGG RPL12 148 2 7 10 1 0
66374 DOLK_GTGGCGGCTACATAGAGCAG DOLK 531 249 125 138 6 29
66375 DOLK_GCCAGGGTAGGACCACACCA DOLK 384 143 96 156 25 12
66376 DOLK_ATACCAGCAGTGCCTCACCA DOLK 625 185 208 166 103 0
66377 DOLK_TACCAGCAGTGCCTCACCAG DOLK 625 272 249 225 95 23
67127 IFNA5_TATGATGCAGGAGGTTGGAG IFNA5 314 321 176 224 229 362
67578 EXOSC3_TAAAGACATGGAACCAGAGA EXOSC3 141 26 9 34 1 5
67579 EXOSC3_TAGGTTGGAGATCTCATCTA EXOSC3 209 102 58 74 27 23
67580 EXOSC3_TGCCGGGCTCCTTGTGACGG EXOSC3 614 170 146 218 27 28
67581 EXOSC3_GTCGCGGCTGAATCTCTCGC EXOSC3 237 72 35 63 6 8
68502 GUCY2F_AAGCTTCCAGATTACCTCAG GUCY2F 272 111 130 133 151 289
68503 GUCY2F_ACTCCATAGCACCTACACTG GUCY2F 348 192 123 193 164 152
68504 GUCY2F_TAAGGAACAACCCAAAGCTC GUCY2F 359 101 95 63 129 310
68505 GUCY2F_GAAGGGACATGACAGACAGA GUCY2F 334 96 68 100 326 145
69790 FAM47B_GGCCCGGGAGAAGACAACCG FAM47B 453 210 118 114 242 250
69791 FAM47B_GGGCCAGGAGATGACAACCG FAM47B 183 87 122 102 178 166
69792 FAM47B_GAGTTATGGGAAGCACCAGG FAM47B 226 187 190 207 269 157
69793 FAM47B_GGAGGATAAGGTATGGACCA FAM47B 245 146 132 163 150 221
1 EGFP_TGGTTGTCGGGCAGCAGCAC EGFP 537 222 150 216 243 115
2 EGFP_GGTTGTCGGGCAGCAGCACG EGFP 210 197 92 125 195 177
3 EGFP_TTCAAGTCCGCCATGCCCGA EGFP 517 423 255 282 329 309
4 EGFP_CGGCGGTCACGAACTCCAGC EGFP 278 167 54 120 165 184
5 EGFP_GGTGCCCATCCTGGTCGAGC EGFP 83 99 41 19 107 103
6 EGFP_GAAGTTCGAGGGCGACACCC EGFP 268 145 153 204 133 295
7 EGFP_CATGCCGAGAGTGATCCCGG EGFP 759 327 273 219 371 289
8 EGFP_TCAGCTCGATGCGGTTCACC EGFP 470 201 197 265 461 338
9 EGFP_GCCGTCGTCCTTGAAGAAGA EGFP 258 83 61 88 261 245
10 EGFP_CAGCTCGATGCGGTTCACCA EGFP 613 169 124 144 205 311
11 EGFP_GAAGGGCATCGACTTCAAGG EGFP 218 193 108 98 145 141
12 EGFP_CCTCGAACTTCACCTCGGCG EGFP 167 216 179 122 170 146
13 EGFP_CTGGACGTAGCCTTCGGGCA EGFP 442 285 222 273 369 440
14 EGFP_ATCCGCCACAACATCGAGGA EGFP 86 120 115 72 226 185
15 EGFP_CGTAGGTGAAGGTGGTCACG EGFP 547 405 354 384 379 761
16 EGFP_CTGCACGCCGTAGGTGAAGG EGFP 323 232 193 178 314 362
17 EGFP_CAACGAGAAGCGCGATCACA EGFP 494 254 134 167 367 370
18 EGFP_TGGAGTTCGTGACCGCCGCC EGFP 514 395 322 271 296 263
19 EGFP_GCCGTCCAGCTCGACCAGGA EGFP 357 110 133 148 160 262
20 EGFP_CAAGTTCAGCGTGTCCGGCG EGFP 450 277 118 201 362 155
21 EGFP_AAGTTCAGCGTGTCCGGCGA EGFP 305 418 247 314 335 298
22 EGFP_GGTCTTTGCTCAGGGCGGAC EGFP 285 114 131 94 53 71
23 LacZ_CAGCTGGCGTAATAGCGAAG LacZ 73 37 33 37 195 243
24 LacZ_CCTTGTGGAGCGACATCCAG LacZ 452 266 164 173 522 398
25 LacZ_GGCACTTCACCGCTTGCCAG LacZ 101 157 69 84 98 94
26 LacZ_CGTTATCGCTATGACGGAAC LacZ 172 107 77 79 138 134
27 LacZ_TTTGCCCGGATAAACGGAAC LacZ 203 68 45 78 143 207
28 LacZ_CCAGACCGTTCATACAGAAC LacZ 313 170 98 82 142 341
29 LacZ_CAATATTGAAACCCACGGCA LacZ 189 209 133 138 166 217
30 LacZ_TCACCGCCGTAAGCCGACCA LacZ 931 320 266 388 925 570
31 LacZ_GAGCGAACGCGTAACGCGAA LacZ 173 17 30 25 29 106
32 LacZ_CACCGCCGTAAGCCGACCAC LacZ 617 276 232 194 271 245
33 LacZ_CAAGACTGTTACCCATCGCG LacZ 280 208 189 179 347 147
34 LacZ_GACGAAGCCGCCCTGTAAAC LacZ 205 141 111 126 293 223
35 LacZ_ACGAAGCCGCCCTGTAAACG LacZ 479 159 145 191 217 59
36 LacZ_CGCCCGGTGCAGTATGAAGG LacZ 423 275 196 239 429 435
37 LacZ_CCGGTGCAGTATGAAGGCGG LacZ 129 104 47 81 42 133
38 LacZ_CGTATTCGCAAAGGATCAGC LacZ 62 52 28 21 15 87
39 LacZ_TTGCCCGATGTACGCGCGCG LacZ 304 155 129 203 146 210
40 LacZ_CCGCGTGCAGCAGATGGCGA LacZ 200 115 77 79 66 170
41 LacZ_CCTTCCCGGCTGTGCCGAAA LacZ 389 125 89 102 161 208
42 LacZ_CCATTTCGGCACAGCCGGGA LacZ 304 166 140 159 278 231
43 LacZ_TGGACCATTTCGGCACAGCC LacZ 377 130 105 100 257 97
44 LacZ_TGCGCAGCCTGAATGGCGAA LacZ 279 89 50 84 111 232
45 LacZ_CATTTCGGCACAGCCGGGAA LacZ 367 109 82 108 297 383
46 LacZ_CCGCCGCCTTCATACTGCAC LacZ 565 241 172 298 491 290
47 LacZ_CATCGGGCAAATAATATCGG LacZ 307 217 101 141 450 256
48 LacZ_GCGCGTCGTGATTAGCGCCG LacZ 39 17 2 0 16 56
49 LacZ_CGCCTTCATACTGCACCGGG LacZ 642 431 301 311 319 321
50 LacZ_CGCCGCCTTCATACTGCACC LacZ 774 314 220 208 384 310
51 LacZ_TCATACTGCACCGGGCGGGA LacZ 422 289 269 195 275 284
52 LacZ_GCCTTCATACTGCACCGGGC LacZ 230 159 124 162 190 152
53 LacZ_AGGGCGGCTTCGTCTGGGAC LacZ 383 229 183 235 237 244
54 LacZ_AACCCGTGGTCGGCTTACGG LacZ 106 104 55 82 114 110
55 LacZ_CTCATCGCCGGTAGCCAGCG LacZ 265 143 108 85 155 242
56 LacZ_GATTCATTGGCACCATGCCG LacZ 131 114 98 81 141 143
57 LacZ_TGTAGCGGCTGATGTTGAAC LacZ 202 145 97 110 97 135
58 LacZ_TCGCACAGCGTGTACCACAG LacZ 579 195 158 196 326 271
59 LacZ_CTGGTTTCCGGCACCAGAAG LacZ 271 162 131 150 205 330
60 LacZ_CGGATAATGCGAACAGCGCA LacZ 400 148 118 149 358 240
T18_C T18_A_Starved T18_B_Starved T18_C_Starved classification
2007 36 42 47 17 essential
2008 7 5 40 43 essential
2009 97 50 82 50 essential
2010 22 3 23 15 essential
3396 11 5 0 0 essential
3397 2 26 42 7 essential
3398 0 0 0 22 essential
3399 35 10 33 159 essential
3464 49 60 42 44 nonessential
3465 152 126 159 127 nonessential
3466 384 304 190 459 nonessential
3467 181 85 86 62 nonessential
3599 302 96 190 140 nonessential
3600 476 318 156 267 nonessential
3601 468 237 210 191 nonessential
3602 361 287 262 445 nonessential
3655 386 170 184 146 nonessential
3656 334 356 661 462 nonessential
3657 428 245 266 210 nonessential
3658 287 89 456 411 nonessential
3951 8 11 55 2 essential
3952 12 23 14 9 essential
3953 104 165 174 155 essential
3954 100 45 98 42 essential
6674 224 106 69 65 nonessential
6675 512 425 362 283 nonessential
6676 410 545 638 511 nonessential
6677 211 584 125 162 nonessential
11161 107 240 175 90 essential
11162 109 153 207 120 essential
12503 3 33 2 17 essential
12504 53 51 16 40 essential
12505 101 94 13 5 essential
12506 41 43 59 97 essential
13759 18 58 11 33 essential
13760 9 8 41 24 essential
13761 14 32 16 0 essential
13762 80 82 59 46 essential
15352 30 26 38 45 essential
15353 16 28 40 37 essential
15354 5 0 0 13 essential
15355 9 19 2 5 essential
17223 54 54 76 64 nonessential
17224 255 164 413 159 nonessential
17225 76 46 115 28 nonessential
17228 306 421 254 130 nonessential
27722 123 93 363 105 essential
27723 17 4 40 1 essential
27724 14 11 19 32 essential
27725 9 15 29 52 essential
27770 11 2 0 0 essential
27771 0 0 24 0 essential
27772 31 13 40 76 essential
27773 30 23 0 1 essential
28014 97 115 151 168 nonessential
28015 219 256 284 229 nonessential
28016 134 97 104 122 nonessential
28017 32 41 60 48 nonessential
28118 85 110 17 10 essential
28119 17 51 1 61 essential
28120 0 26 12 10 essential
28121 66 35 28 66 essential
30909 182 135 146 162 nonessential
30910 92 128 129 116 nonessential
30911 186 140 201 213 nonessential
30912 130 76 247 79 nonessential
32765 267 211 127 99 nonessential
32766 389 170 391 401 nonessential
32767 268 104 82 147 nonessential
32768 238 47 67 276 nonessential
33931 236 144 142 77 nonessential
33932 357 503 294 225 nonessential
33933 349 472 554 173 nonessential
36313 170 217 392 479 nonessential
36314 110 67 102 210 nonessential
36315 200 108 208 137 nonessential
36316 378 215 140 97 nonessential
37544 92 21 50 55 nonessential
37545 177 257 488 520 nonessential
37546 137 110 235 136 nonessential
37547 119 184 246 129 nonessential
37648 28 63 133 32 essential
37649 84 51 30 42 essential
37650 26 25 2 5 essential
37651 17 0 0 15 essential
37708 210 236 229 119 nonessential
37709 249 134 222 233 nonessential
37710 158 98 348 98 nonessential
37711 284 336 622 317 nonessential
47639 7 31 87 62 essential
47640 101 43 109 19 essential
47641 73 84 48 20 essential
47642 40 22 27 27 essential
48225 360 260 598 256 nonessential
48226 221 155 134 167 nonessential
48227 516 219 361 319 nonessential
48228 172 168 138 300 nonessential
48401 205 212 142 79 essential
48402 158 160 58 89 essential
48403 0 12 2 0 essential
48404 0 11 0 15 essential
53441 295 231 177 155 nonessential
53442 387 312 303 337 nonessential
53443 224 179 197 164 nonessential
53444 665 368 652 557 nonessential
58856 102 268 85 114 essential
58857 42 54 44 49 essential
58858 0 30 42 5 essential
58859 27 25 10 4 essential
59238 205 211 240 142 essential
59239 16 12 54 20 essential
59240 80 50 52 95 essential
59241 19 11 5 55 essential
62425 11 27 13 2 essential
62426 141 143 220 69 essential
62427 76 304 53 73 essential
62428 38 0 57 19 essential
66194 14 2 5 0 essential
66195 5 1 0 0 essential
66196 2 5 0 8 essential
66197 4 0 2 0 essential
66374 23 10 17 26 essential
66375 35 20 45 43 essential
66376 35 21 0 8 essential
66377 4 5 26 77 essential
67127 252 402 272 284 nonessential
67578 2 0 12 17 essential
67579 43 36 28 10 essential
67580 54 24 127 120 essential
67581 20 16 119 62 essential
68502 215 164 325 196 nonessential
68503 170 170 240 46 nonessential
68504 74 100 112 123 nonessential
68505 129 128 184 193 nonessential
69790 146 142 187 175 nonessential
69791 73 154 80 168 nonessential
69792 326 149 174 267 nonessential
69793 149 149 181 197 nonessential
1 304 277 319 240 unknown
2 115 96 139 235 unknown
3 433 371 565 428 unknown
4 65 169 147 68 unknown
5 44 19 69 73 unknown
6 228 339 131 173 unknown
7 430 268 428 278 unknown
8 268 272 278 221 unknown
9 143 87 163 93 unknown
10 218 200 209 189 unknown
11 289 57 172 219 unknown
12 158 158 98 236 unknown
13 308 302 342 290 unknown
14 195 152 357 43 unknown
15 357 378 366 529 unknown
16 571 179 464 130 unknown
17 387 105 360 384 unknown
18 364 379 511 341 unknown
19 269 102 67 90 unknown
20 241 184 342 343 unknown
21 482 542 472 411 unknown
22 229 192 165 287 unknown
23 123 100 43 53 unknown
24 268 291 333 127 unknown
25 172 138 143 159 unknown
26 103 220 180 35 unknown
27 157 170 149 51 unknown
28 126 156 109 206 unknown
29 140 286 175 182 unknown
30 648 431 481 286 unknown
31 52 50 136 13 unknown
32 231 161 358 120 unknown
33 199 120 231 211 unknown
34 264 144 244 497 unknown
35 287 259 178 172 unknown
36 324 254 397 351 unknown
37 81 66 76 49 unknown
38 114 12 25 17 unknown
39 276 127 274 252 unknown
40 190 137 211 84 unknown
41 190 187 175 94 unknown
42 289 239 523 473 unknown
43 231 180 133 145 unknown
44 191 150 185 60 unknown
45 338 181 203 180 unknown
46 394 402 313 258 unknown
47 278 121 241 253 unknown
48 16 52 69 11 unknown
49 521 306 556 369 unknown
50 471 504 301 420 unknown
51 251 264 255 330 unknown
52 122 173 398 243 unknown
53 233 334 314 354 unknown
54 192 162 225 76 unknown
55 194 216 165 84 unknown
56 182 131 314 151 unknown
57 515 170 457 166 unknown
58 249 150 133 319 unknown
59 144 128 298 197 unknown
60 150 207 448 105 unknown
can get bagel statistics sgrna-level
Code
get_bagel_statistics(data = test_classified_sgrna)
Message <simpleMessage>
Building BAGEL classification statistics...
Output
# A tibble: 10 x 17
sample max_essential max_nonessential max_unknown mean_essential
<chr> <dbl> <dbl> <dbl> <dbl>
1 T0_- 1182 915 931 343.
2 T18_A 314 793 925 50.2
3 T18_A_Starved 304 584 542 49.0
4 T18_B 294 636 761 43.6
5 T18_B_Starved 363 661 565 50.7
6 T18_C 205 665 648 42.8
7 T18_C_Starved 159 557 529 39.6
8 T3_A 360 492 431 113.
9 T3_B 249 328 354 80.1
10 T3_C 250 409 388 95.2
# i 12 more variables: mean_nonessential <dbl>, mean_unknown <dbl>,
# median_essential <dbl>, median_nonessential <dbl>, median_unknown <dbl>,
# min_essential <dbl>, min_nonessential <dbl>, min_unknown <dbl>,
# n_genes_essential <dbl>, n_genes_nonessential <dbl>, n_genes_unknown <dbl>,
# total_genes <dbl>
can get bagel statistics gene-level
Code
get_bagel_statistics(data = test_classified_gene, is_gene = T)
Message <simpleMessage>
Building BAGEL classification statistics...
Output
# A tibble: 10 x 17
sample max_essential max_nonessential max_unknown mean_essential
<chr> <dbl> <dbl> <dbl> <dbl>
1 T0_- 1182 915 931 343.
2 T18_A 314 793 925 50.2
3 T18_A_Starved 304 584 542 49.0
4 T18_B 294 636 761 43.6
5 T18_B_Starved 363 661 565 50.7
6 T18_C 205 665 648 42.8
7 T18_C_Starved 159 557 529 39.6
8 T3_A 360 492 431 113.
9 T3_B 249 328 354 80.1
10 T3_C 250 409 388 95.2
# i 12 more variables: mean_nonessential <dbl>, mean_unknown <dbl>,
# median_essential <dbl>, median_nonessential <dbl>, median_unknown <dbl>,
# min_essential <dbl>, min_nonessential <dbl>, min_unknown <dbl>,
# n_genes_essential <dbl>, n_genes_nonessential <dbl>, n_genes_unknown <dbl>,
# total_genes <dbl>
can get bagel statistics gene-level fold changes
Code
get_bagel_statistics(data = test_classified_fc_gene_narrow, is_gene = T, is_fc = T)
Message <simpleMessage>
Building BAGEL classification statistics...
Output
# A tibble: 3 x 19
sample NNMD Essential.Glass.Delta max_essential max_nonessential max_unknown
<chr> <chr> <chr> <dbl> <dbl> <dbl>
1 T3_A -2.502 2.553 -0.290 0.0318 -0.655
2 T3_B -2.430 4.084 -0.848 -0.732 -1.16
3 T3_C -1.807 3.606 -0.488 -0.486 -1.06
# i 13 more variables: mean_essential <dbl>, mean_nonessential <dbl>,
# mean_unknown <dbl>, median_essential <dbl>, median_nonessential <dbl>,
# median_unknown <dbl>, min_essential <dbl>, min_nonessential <dbl>,
# min_unknown <dbl>, n_genes_essential <dbl>, n_genes_nonessential <dbl>,
# n_genes_unknown <dbl>, total_genes <dbl>
can prepare essentiality data
Code
prepare_essentiality_data(data = test_avg_classified_fc_gene)
Output
$essentiality
ACTR10 BYSL CCDC84 CDCP2 CELA3A COPB1 CRX CST8 DEFB123 DOLK
1 1 1 0 0 1 0 0 0 1
ERCC2 EXOSC3 FAM47B GFM1 GJA8 GUCY2F HYPK IFNA5 IL9 MCM3
1 1 0 1 0 0 1 0 0 1
MFRP NCBP2 NOP56 NPHS2 OR10A2 OR10S1 PANX3 PDILT PPA1 RFC2
0 1 1 0 0 0 0 0 1 1
RPL12 RPL18 SNRPD2 TMEM207 UBE2N WDR25
1 1 1 0 1 1
$predictor
[1] -2.2014271 -1.8236720 -1.1793501 -0.8099540 -0.5105452 -2.7617258
[7] -0.7722082 -1.2019199 -1.9291828 -1.5892816 -1.8663399 -2.0399960
[13] -0.8658798 -1.3854727 -1.1666279 -1.5530624 -2.1071931 -0.4293259
[19] -1.4566546 -1.1754400 -1.4115151 -2.3198319 -2.1092655 -0.9654381
[25] -1.2053156 -0.9958179 -0.8259206 -1.3746929 -1.2871011 -2.7677641
[31] -4.7692111 -2.6629914 -1.9312815 -1.1161930 -0.5420802 -1.4475384
$min
[1] -4.769211
$modified_predictor
[1] 2.567784 2.945539 3.589861 3.959257 4.258666 2.007485 3.997003 3.567291
[9] 2.840028 3.179929 2.902871 2.729215 3.903331 3.383738 3.602583 3.216149
[17] 2.662018 4.339885 3.312557 3.593771 3.357696 2.449379 2.659946 3.803773
[25] 3.563895 3.773393 3.943291 3.394518 3.482110 2.001447 0.000000 2.106220
[33] 2.837930 3.653018 4.227131 3.321673
can process ROC
Code
process_roc(test_screen_roc, test_essentiality_data[["min"]])
Output
thresholds specificity sensitivity ppv
best_prec -1.930232 1 0.5263158 1
can plot ROC
Code
p$data
Output
FPR TPR
1 1.00000000 1.00000000
2 0.94117647 1.00000000
3 0.88235294 1.00000000
4 0.88235294 0.94736842
5 0.82352941 0.94736842
6 0.76470588 0.94736842
7 0.70588235 0.94736842
8 0.64705882 0.94736842
9 0.58823529 0.94736842
10 0.52941176 0.94736842
11 0.47058824 0.94736842
12 0.41176471 0.94736842
13 0.41176471 0.89473684
14 0.41176471 0.84210526
15 0.35294118 0.84210526
16 0.29411765 0.84210526
17 0.29411765 0.78947368
18 0.23529412 0.78947368
19 0.23529412 0.73684211
20 0.17647059 0.73684211
21 0.17647059 0.68421053
22 0.11764706 0.68421053
23 0.05882353 0.68421053
24 0.05882353 0.63157895
25 0.05882353 0.57894737
26 0.05882353 0.52631579
27 0.00000000 0.52631579
28 0.00000000 0.47368421
29 0.00000000 0.42105263
30 0.00000000 0.36842105
31 0.00000000 0.31578947
32 0.00000000 0.26315789
33 0.00000000 0.21052632
34 0.00000000 0.15789474
35 0.00000000 0.10526316
36 0.00000000 0.05263158
37 0.00000000 0.00000000
Code
p$layers
Output
[[1]]
geom_line: na.rm = FALSE, orientation = NA
stat_identity: na.rm = FALSE
position_identity
[[2]]
mapping: x = ~x, y = ~y
geom_text: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can average guide BFs
Code
average_guide_bfs(data = test_bf_matrix, gene_column = 1, data_columns = 2)
Output
# A tibble: 2 x 2
gene mean
<chr> <dbl>
1 ABCC3 -1.26
2 ABL1 -1.71
cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.
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can add bagel_classification
Code
add_bagel_classifications(data = test_count_matrix, gene_column = 2, ess = ess,
noness = noness)
Output
sgRNA gene T0_- T3_A T3_B T3_C T18_A T18_B
2007 PPA1_TTTAGACTTGGGAAGACCCA PPA1 277 92 64 67 10 27
2008 PPA1_GTTGCATGAAGACATACCTG PPA1 267 143 108 46 62 2
2009 PPA1_TGGTAGTTGAAGTACCACGC PPA1 98 45 85 60 72 75
2010 PPA1_TATGAGCGGCTTCAGCACCG PPA1 388 261 179 159 20 0
3396 CCDC84_AAGAAGGTCTGGCGGCACAG CCDC84 321 238 108 181 0 9
3397 CCDC84_GTGCGGGAACACCTGAGCCA CCDC84 321 114 70 66 8 31
3398 CCDC84_CTGGTGGGAGAACAAAGCTG CCDC84 440 236 107 164 31 51
3399 CCDC84_GGAATCCAAACCTTTCACCA CCDC84 116 83 83 111 55 52
3464 MFRP_AGACGAAGACCACCAGGAGG MFRP 214 38 30 76 61 75
3465 MFRP_GGGACAGAGGGACCTACCTG MFRP 285 115 106 147 129 95
3466 MFRP_CATAGCCCACTGCCTGCCGG MFRP 618 492 312 352 398 287
3467 MFRP_GGAGGCAACAGAATCGAGCA MFRP 166 72 60 51 280 78
3599 OR10S1_GTTGCGCATCCGCACAGCCC OR10S1 185 122 104 134 268 164
3600 OR10S1_AGACAAACAGGCATCCAGGA OR10S1 526 218 165 143 377 326
3601 OR10S1_AGTGGTACATGGGTAAGCTG OR10S1 178 206 153 150 218 162
3602 OR10S1_TGAGAAGATGACCATGACAA OR10S1 592 197 187 176 209 404
3655 PANX3_CCAGACGCAGTCCTTTGAGG PANX3 528 233 173 204 250 233
3656 PANX3_CCAGCAGGAGCTGTCCACGT PANX3 698 321 225 250 317 239
3657 PANX3_TGAACAGCAGATCGGAGCTG PANX3 373 329 140 193 444 206
3658 PANX3_AAGGTATAGGTAAGTGGCGG PANX3 276 378 275 409 111 338
3951 COPB1_AGAAGGAATCCTCTCAAGGG COPB1 164 18 31 23 20 12
3952 COPB1_TATTGTGCTAGGATTTACCG COPB1 317 24 35 15 20 41
3953 COPB1_AGAAGGATGCAAGTTGCAAA COPB1 140 58 63 89 66 122
3954 COPB1_ATAACCAGAAACCATGACGG COPB1 416 49 40 24 13 39
6674 OR10A2_GACATTTCTAACCATCTACC OR10A2 195 71 69 56 93 173
6675 OR10A2_CATCTACCTGGTCACCCTGA OR10A2 544 265 265 286 326 440
6676 OR10A2_CATCAGGGTGACCAGGTAGA OR10A2 829 387 328 320 402 636
6677 OR10A2_GATGAGGCAGTTTCCCATCA OR10A2 206 103 100 111 93 296
11161 UBE2N_TTCTGTCTACAGCTAGAGCA UBE2N 342 235 136 203 314 90
11162 UBE2N_AGATACCTGTTTCTATGGCT UBE2N 221 215 171 189 80 84
12503 WDR25_ACAGCGGCAGGCATTAAGCA WDR25 583 183 115 159 20 56
12504 WDR25_CGAAGTCAAAGCCACCACTG WDR25 1182 335 246 207 27 34
12505 WDR25_GGAACTCGGAGCCTTCCCGG WDR25 83 63 63 77 1 65
12506 WDR25_CATCCGGTAGGGCCACACAG WDR25 527 262 174 199 161 75
13759 ACTR10_ACTACCATGCCGCTCTACGA ACTR10 320 86 40 123 0 18
13760 ACTR10_ATTCGATAATCACAACTCGG ACTR10 182 54 15 32 6 16
13761 ACTR10_ATATCCACAATCTAGGACCA ACTR10 353 72 53 57 35 1
13762 ACTR10_ACAGAGCCTTCCCTCAGTGA ACTR10 424 127 146 152 47 102
15352 HYPK_AAGCCACGGAAACATGACAG HYPK 276 43 43 90 8 21
15353 HYPK_GAAACATGACAGCGGTGCGG HYPK 291 120 109 150 128 34
15354 HYPK_GCGGGTCACCGACTATGCAG HYPK 192 43 31 6 0 0
15355 HYPK_GCGGGAACACATGGGCAACG HYPK 314 150 75 82 21 17
17223 PDILT_ATGACTCCAAACGTTAGCTC PDILT 199 99 58 27 116 91
17224 PDILT_GAAGAAGCCAACGATGACCA PDILT 310 200 132 150 239 236
17225 PDILT_AGTGGACATTACCATAGAGA PDILT 119 48 38 36 49 29
17228 PDILT_CAAGCCTGTGCACATCCTGG PDILT 518 286 203 240 145 166
27722 ERCC2_ATCCAGGTTGTAGATGCCAG ERCC2 491 360 205 250 182 222
27723 ERCC2_AAGGAACAGGTGCTCACCTC ERCC2 426 98 85 54 13 3
27724 ERCC2_TTATCGGCAGGCATATCCGC ERCC2 532 151 101 115 30 4
27725 ERCC2_GCGGGAGCTCAAACGCACGC ERCC2 280 94 58 66 52 5
27770 SNRPD2_TCTCCAAGATGTTCCTGCGC SNRPD2 2 2 8 19 0 0
27771 SNRPD2_CATGGTGCTGGAGAACGTGA SNRPD2 215 25 12 18 58 8
27772 SNRPD2_ACCCAGCACTCACCTATCGA SNRPD2 208 39 24 31 56 112
27773 SNRPD2_GAGGAGGAGGAATTTAACAC SNRPD2 257 33 22 45 35 35
28014 CRX_TAGGAATCTGAGATGCCCAG CRX 90 183 128 161 247 72
28015 CRX_GCTCGGAGACCCATAGGCGG CRX 330 253 217 301 279 202
28016 CRX_GGCCAGGGAAGGTCCCACGG CRX 245 127 87 137 42 85
28017 CRX_GAAATTCACCTACAATCCCA CRX 137 30 18 30 49 36
28118 RPL18_TCGAGCGTGCCAGAGGCCGA RPL18 523 68 60 74 47 49
28119 RPL18_CCTTCCCTAGGTCCTCGCAA RPL18 241 36 39 30 2 34
28120 RPL18_CAGCCGCATCCTCAGGGCAG RPL18 458 82 50 58 12 18
28121 RPL18_AGTGGACATCCGCCATAACA RPL18 298 95 49 79 74 52
30909 GJA8_TGGGCGACTGGAGTTTCCTG GJA8 523 250 117 178 267 260
30910 GJA8_AGAGGAGGGAGCCGAACCCG GJA8 308 239 109 149 187 61
30911 GJA8_AGCAGAGAGGCTGACCACGG GJA8 408 162 188 176 137 193
30912 GJA8_GGAGAAGGTGGCCGTGCCAG GJA8 315 181 144 188 249 162
32765 NPHS2_GCAAAGACAAGCCAAAGTGC NPHS2 354 128 121 174 300 264
32766 NPHS2_CAGGAAGCAGATGTCCCAGT NPHS2 538 273 206 235 542 404
32767 NPHS2_GAGGACAAGAAGCCACTCAC NPHS2 185 91 93 82 172 107
32768 NPHS2_GTTGGAGAGCGAGCGGCCCG NPHS2 174 205 115 126 248 69
33931 CELA3A_GAGGGATCTGACCTACCAGG CELA3A 133 166 140 156 79 171
33932 CELA3A_TGAGTACAACCTTGCTGTGA CELA3A 476 414 285 296 500 351
33933 CELA3A_GCAGTGCTTATAGTCCACCA CELA3A 423 215 146 199 321 259
36313 CDCP2_CAGACCGCAGCACCACCCGC CDCP2 530 396 209 183 360 298
36314 CDCP2_GGTGTTCGTGGACTTCCAGG CDCP2 128 220 125 128 141 52
36315 CDCP2_ATGGAAGGTGAGCAGCACCG CDCP2 155 143 127 145 119 131
36316 CDCP2_AGGGCTCCAGGCCCAAGCCA CDCP2 459 99 90 105 250 169
37544 CST8_GGACCATGCCCAGGTGCCGG CST8 179 110 52 43 144 36
37545 CST8_CCACAGACACTGCTTCACGT CST8 915 249 252 297 283 348
37546 CST8_AAGGCTTTCTGCAATCGCTG CST8 276 202 118 147 80 231
37547 CST8_GAATGGTGAATTCACTGTGA CST8 132 147 66 60 51 265
37648 NOP56_GCTGGCGCTGAAGGAAGTGG NOP56 294 108 44 75 76 51
37649 NOP56_AATGCCAACGCCGTGTCTGA NOP56 528 147 95 190 28 64
37650 NOP56_GATTGGTGCCGCAATACAGG NOP56 181 70 35 82 23 4
37651 NOP56_CAGCTTGTAAAGCACAGCTG NOP56 167 60 8 24 48 1
37708 DEFB123_GCACAGTCAAAGTCAGCAAA DEFB123 492 141 103 76 179 270
37709 DEFB123_CAGGTGGCACCCAAAGATGC DEFB123 556 264 143 118 247 249
37710 DEFB123_CCGTTACAGATGCTCCAAGA DEFB123 493 151 94 90 180 121
37711 DEFB123_AATGGCCACCACCTTTCTTT DEFB123 644 333 157 207 379 209
47639 GFM1_TTAATTGGAAGGCCTGCCGA GFM1 435 258 159 155 143 22
47640 GFM1_AATGGGCTCCAACCCAGCCA GFM1 509 136 78 110 109 110
47641 GFM1_AGCGTTTATGCAGATACCCA GFM1 166 111 98 111 16 44
47642 GFM1_ATTCAATTAGCTCCTGCCGG GFM1 664 265 246 240 32 30
48225 TMEM207_TGAAGGTGAATTCCAACAGT TMEM207 572 196 115 202 404 239
48226 TMEM207_TGATTCTCACAGGCGCACCA TMEM207 264 103 107 112 149 160
48227 TMEM207_TTGGTGGCAGCTCTTCTCTG TMEM207 404 381 228 324 275 205
48228 TMEM207_ATGACCAACACCCTAATGGC TMEM207 325 197 175 130 99 177
48401 NCBP2_ACTGGCACAGAACCAGTGAG NCBP2 299 130 60 87 128 231
48402 NCBP2_GAGGGCAGGCAATACGGCCG NCBP2 244 99 71 77 141 69
48403 NCBP2_GTACTGGCTCAGCTCCACGT NCBP2 449 51 53 82 22 0
48404 NCBP2_GCTGCGCAGCGACTCCTACG NCBP2 397 36 50 58 0 0
53441 IL9_TGTGCTCCGTGGCAGGCCAG IL9 504 346 184 242 329 219
53442 IL9_TGCCACGGAGCACAGGAGCA IL9 649 312 133 196 497 214
53443 IL9_CAGGGCAGAGGTAAGGACCA IL9 834 225 166 211 376 156
53444 IL9_TGTCAAGATGCTTCTGGCCA IL9 725 361 308 379 793 569
58856 BYSL_TCGCGGGACAGGAGAAGCGG BYSL 682 129 79 71 33 46
58857 BYSL_GGAGTGGCCCACCCTGGAGA BYSL 332 83 72 73 149 31
58858 BYSL_GGTCCTAGAAGTGTACAGGG BYSL 340 139 88 96 24 18
58859 BYSL_GTATTATCTAAGTACCGCAG BYSL 31 13 20 34 1 15
59238 MCM3_TCAGCCCTCTTTCTCTGCTG MCM3 481 196 161 226 182 294
59239 MCM3_AAGAAGGGAGGCTACACCTC MCM3 108 74 86 90 68 32
59240 MCM3_GGTAGGATAGACAGAGCTGG MCM3 220 110 80 76 71 68
59241 MCM3_GAAGGCAACCAGCTCCTCAA MCM3 185 52 46 79 49 34
62425 RFC2_TGTACCGGAGGACTGCACAG RFC2 409 34 19 27 0 0
62426 RFC2_TTTCTTCTCAGCATGACCGA RFC2 420 157 68 127 102 117
62427 RFC2_TGTGCCCAACATCATCATTG RFC2 615 134 89 110 77 91
62428 RFC2_GAGGTGGAGGCCGTCTGTGG RFC2 440 93 52 61 27 10
66194 RPL12_TCTTCTGCAGTTAAACACAG RPL12 208 6 15 9 78 79
66195 RPL12_GGGATAACGTACCAGACCCA RPL12 218 11 2 5 1 0
66196 RPL12_GGATAACGTACCAGACCCAG RPL12 329 5 20 19 7 22
66197 RPL12_GATAACGTACCAGACCCAGG RPL12 148 2 7 10 1 0
66374 DOLK_GTGGCGGCTACATAGAGCAG DOLK 531 249 125 138 6 29
66375 DOLK_GCCAGGGTAGGACCACACCA DOLK 384 143 96 156 25 12
66376 DOLK_ATACCAGCAGTGCCTCACCA DOLK 625 185 208 166 103 0
66377 DOLK_TACCAGCAGTGCCTCACCAG DOLK 625 272 249 225 95 23
67127 IFNA5_TATGATGCAGGAGGTTGGAG IFNA5 314 321 176 224 229 362
67578 EXOSC3_TAAAGACATGGAACCAGAGA EXOSC3 141 26 9 34 1 5
67579 EXOSC3_TAGGTTGGAGATCTCATCTA EXOSC3 209 102 58 74 27 23
67580 EXOSC3_TGCCGGGCTCCTTGTGACGG EXOSC3 614 170 146 218 27 28
67581 EXOSC3_GTCGCGGCTGAATCTCTCGC EXOSC3 237 72 35 63 6 8
68502 GUCY2F_AAGCTTCCAGATTACCTCAG GUCY2F 272 111 130 133 151 289
68503 GUCY2F_ACTCCATAGCACCTACACTG GUCY2F 348 192 123 193 164 152
68504 GUCY2F_TAAGGAACAACCCAAAGCTC GUCY2F 359 101 95 63 129 310
68505 GUCY2F_GAAGGGACATGACAGACAGA GUCY2F 334 96 68 100 326 145
69790 FAM47B_GGCCCGGGAGAAGACAACCG FAM47B 453 210 118 114 242 250
69791 FAM47B_GGGCCAGGAGATGACAACCG FAM47B 183 87 122 102 178 166
69792 FAM47B_GAGTTATGGGAAGCACCAGG FAM47B 226 187 190 207 269 157
69793 FAM47B_GGAGGATAAGGTATGGACCA FAM47B 245 146 132 163 150 221
1 EGFP_TGGTTGTCGGGCAGCAGCAC EGFP 537 222 150 216 243 115
2 EGFP_GGTTGTCGGGCAGCAGCACG EGFP 210 197 92 125 195 177
3 EGFP_TTCAAGTCCGCCATGCCCGA EGFP 517 423 255 282 329 309
4 EGFP_CGGCGGTCACGAACTCCAGC EGFP 278 167 54 120 165 184
5 EGFP_GGTGCCCATCCTGGTCGAGC EGFP 83 99 41 19 107 103
6 EGFP_GAAGTTCGAGGGCGACACCC EGFP 268 145 153 204 133 295
7 EGFP_CATGCCGAGAGTGATCCCGG EGFP 759 327 273 219 371 289
8 EGFP_TCAGCTCGATGCGGTTCACC EGFP 470 201 197 265 461 338
9 EGFP_GCCGTCGTCCTTGAAGAAGA EGFP 258 83 61 88 261 245
10 EGFP_CAGCTCGATGCGGTTCACCA EGFP 613 169 124 144 205 311
11 EGFP_GAAGGGCATCGACTTCAAGG EGFP 218 193 108 98 145 141
12 EGFP_CCTCGAACTTCACCTCGGCG EGFP 167 216 179 122 170 146
13 EGFP_CTGGACGTAGCCTTCGGGCA EGFP 442 285 222 273 369 440
14 EGFP_ATCCGCCACAACATCGAGGA EGFP 86 120 115 72 226 185
15 EGFP_CGTAGGTGAAGGTGGTCACG EGFP 547 405 354 384 379 761
16 EGFP_CTGCACGCCGTAGGTGAAGG EGFP 323 232 193 178 314 362
17 EGFP_CAACGAGAAGCGCGATCACA EGFP 494 254 134 167 367 370
18 EGFP_TGGAGTTCGTGACCGCCGCC EGFP 514 395 322 271 296 263
19 EGFP_GCCGTCCAGCTCGACCAGGA EGFP 357 110 133 148 160 262
20 EGFP_CAAGTTCAGCGTGTCCGGCG EGFP 450 277 118 201 362 155
21 EGFP_AAGTTCAGCGTGTCCGGCGA EGFP 305 418 247 314 335 298
22 EGFP_GGTCTTTGCTCAGGGCGGAC EGFP 285 114 131 94 53 71
23 LacZ_CAGCTGGCGTAATAGCGAAG LacZ 73 37 33 37 195 243
24 LacZ_CCTTGTGGAGCGACATCCAG LacZ 452 266 164 173 522 398
25 LacZ_GGCACTTCACCGCTTGCCAG LacZ 101 157 69 84 98 94
26 LacZ_CGTTATCGCTATGACGGAAC LacZ 172 107 77 79 138 134
27 LacZ_TTTGCCCGGATAAACGGAAC LacZ 203 68 45 78 143 207
28 LacZ_CCAGACCGTTCATACAGAAC LacZ 313 170 98 82 142 341
29 LacZ_CAATATTGAAACCCACGGCA LacZ 189 209 133 138 166 217
30 LacZ_TCACCGCCGTAAGCCGACCA LacZ 931 320 266 388 925 570
31 LacZ_GAGCGAACGCGTAACGCGAA LacZ 173 17 30 25 29 106
32 LacZ_CACCGCCGTAAGCCGACCAC LacZ 617 276 232 194 271 245
33 LacZ_CAAGACTGTTACCCATCGCG LacZ 280 208 189 179 347 147
34 LacZ_GACGAAGCCGCCCTGTAAAC LacZ 205 141 111 126 293 223
35 LacZ_ACGAAGCCGCCCTGTAAACG LacZ 479 159 145 191 217 59
36 LacZ_CGCCCGGTGCAGTATGAAGG LacZ 423 275 196 239 429 435
37 LacZ_CCGGTGCAGTATGAAGGCGG LacZ 129 104 47 81 42 133
38 LacZ_CGTATTCGCAAAGGATCAGC LacZ 62 52 28 21 15 87
39 LacZ_TTGCCCGATGTACGCGCGCG LacZ 304 155 129 203 146 210
40 LacZ_CCGCGTGCAGCAGATGGCGA LacZ 200 115 77 79 66 170
41 LacZ_CCTTCCCGGCTGTGCCGAAA LacZ 389 125 89 102 161 208
42 LacZ_CCATTTCGGCACAGCCGGGA LacZ 304 166 140 159 278 231
43 LacZ_TGGACCATTTCGGCACAGCC LacZ 377 130 105 100 257 97
44 LacZ_TGCGCAGCCTGAATGGCGAA LacZ 279 89 50 84 111 232
45 LacZ_CATTTCGGCACAGCCGGGAA LacZ 367 109 82 108 297 383
46 LacZ_CCGCCGCCTTCATACTGCAC LacZ 565 241 172 298 491 290
47 LacZ_CATCGGGCAAATAATATCGG LacZ 307 217 101 141 450 256
48 LacZ_GCGCGTCGTGATTAGCGCCG LacZ 39 17 2 0 16 56
49 LacZ_CGCCTTCATACTGCACCGGG LacZ 642 431 301 311 319 321
50 LacZ_CGCCGCCTTCATACTGCACC LacZ 774 314 220 208 384 310
51 LacZ_TCATACTGCACCGGGCGGGA LacZ 422 289 269 195 275 284
52 LacZ_GCCTTCATACTGCACCGGGC LacZ 230 159 124 162 190 152
53 LacZ_AGGGCGGCTTCGTCTGGGAC LacZ 383 229 183 235 237 244
54 LacZ_AACCCGTGGTCGGCTTACGG LacZ 106 104 55 82 114 110
55 LacZ_CTCATCGCCGGTAGCCAGCG LacZ 265 143 108 85 155 242
56 LacZ_GATTCATTGGCACCATGCCG LacZ 131 114 98 81 141 143
57 LacZ_TGTAGCGGCTGATGTTGAAC LacZ 202 145 97 110 97 135
58 LacZ_TCGCACAGCGTGTACCACAG LacZ 579 195 158 196 326 271
59 LacZ_CTGGTTTCCGGCACCAGAAG LacZ 271 162 131 150 205 330
60 LacZ_CGGATAATGCGAACAGCGCA LacZ 400 148 118 149 358 240
T18_C T18_A_Starved T18_B_Starved T18_C_Starved classification
2007 36 42 47 17 essential
2008 7 5 40 43 essential
2009 97 50 82 50 essential
2010 22 3 23 15 essential
3396 11 5 0 0 essential
3397 2 26 42 7 essential
3398 0 0 0 22 essential
3399 35 10 33 159 essential
3464 49 60 42 44 nonessential
3465 152 126 159 127 nonessential
3466 384 304 190 459 nonessential
3467 181 85 86 62 nonessential
3599 302 96 190 140 nonessential
3600 476 318 156 267 nonessential
3601 468 237 210 191 nonessential
3602 361 287 262 445 nonessential
3655 386 170 184 146 nonessential
3656 334 356 661 462 nonessential
3657 428 245 266 210 nonessential
3658 287 89 456 411 nonessential
3951 8 11 55 2 essential
3952 12 23 14 9 essential
3953 104 165 174 155 essential
3954 100 45 98 42 essential
6674 224 106 69 65 nonessential
6675 512 425 362 283 nonessential
6676 410 545 638 511 nonessential
6677 211 584 125 162 nonessential
11161 107 240 175 90 essential
11162 109 153 207 120 essential
12503 3 33 2 17 essential
12504 53 51 16 40 essential
12505 101 94 13 5 essential
12506 41 43 59 97 essential
13759 18 58 11 33 essential
13760 9 8 41 24 essential
13761 14 32 16 0 essential
13762 80 82 59 46 essential
15352 30 26 38 45 essential
15353 16 28 40 37 essential
15354 5 0 0 13 essential
15355 9 19 2 5 essential
17223 54 54 76 64 nonessential
17224 255 164 413 159 nonessential
17225 76 46 115 28 nonessential
17228 306 421 254 130 nonessential
27722 123 93 363 105 essential
27723 17 4 40 1 essential
27724 14 11 19 32 essential
27725 9 15 29 52 essential
27770 11 2 0 0 essential
27771 0 0 24 0 essential
27772 31 13 40 76 essential
27773 30 23 0 1 essential
28014 97 115 151 168 nonessential
28015 219 256 284 229 nonessential
28016 134 97 104 122 nonessential
28017 32 41 60 48 nonessential
28118 85 110 17 10 essential
28119 17 51 1 61 essential
28120 0 26 12 10 essential
28121 66 35 28 66 essential
30909 182 135 146 162 nonessential
30910 92 128 129 116 nonessential
30911 186 140 201 213 nonessential
30912 130 76 247 79 nonessential
32765 267 211 127 99 nonessential
32766 389 170 391 401 nonessential
32767 268 104 82 147 nonessential
32768 238 47 67 276 nonessential
33931 236 144 142 77 nonessential
33932 357 503 294 225 nonessential
33933 349 472 554 173 nonessential
36313 170 217 392 479 nonessential
36314 110 67 102 210 nonessential
36315 200 108 208 137 nonessential
36316 378 215 140 97 nonessential
37544 92 21 50 55 nonessential
37545 177 257 488 520 nonessential
37546 137 110 235 136 nonessential
37547 119 184 246 129 nonessential
37648 28 63 133 32 essential
37649 84 51 30 42 essential
37650 26 25 2 5 essential
37651 17 0 0 15 essential
37708 210 236 229 119 nonessential
37709 249 134 222 233 nonessential
37710 158 98 348 98 nonessential
37711 284 336 622 317 nonessential
47639 7 31 87 62 essential
47640 101 43 109 19 essential
47641 73 84 48 20 essential
47642 40 22 27 27 essential
48225 360 260 598 256 nonessential
48226 221 155 134 167 nonessential
48227 516 219 361 319 nonessential
48228 172 168 138 300 nonessential
48401 205 212 142 79 essential
48402 158 160 58 89 essential
48403 0 12 2 0 essential
48404 0 11 0 15 essential
53441 295 231 177 155 nonessential
53442 387 312 303 337 nonessential
53443 224 179 197 164 nonessential
53444 665 368 652 557 nonessential
58856 102 268 85 114 essential
58857 42 54 44 49 essential
58858 0 30 42 5 essential
58859 27 25 10 4 essential
59238 205 211 240 142 essential
59239 16 12 54 20 essential
59240 80 50 52 95 essential
59241 19 11 5 55 essential
62425 11 27 13 2 essential
62426 141 143 220 69 essential
62427 76 304 53 73 essential
62428 38 0 57 19 essential
66194 14 2 5 0 essential
66195 5 1 0 0 essential
66196 2 5 0 8 essential
66197 4 0 2 0 essential
66374 23 10 17 26 essential
66375 35 20 45 43 essential
66376 35 21 0 8 essential
66377 4 5 26 77 essential
67127 252 402 272 284 nonessential
67578 2 0 12 17 essential
67579 43 36 28 10 essential
67580 54 24 127 120 essential
67581 20 16 119 62 essential
68502 215 164 325 196 nonessential
68503 170 170 240 46 nonessential
68504 74 100 112 123 nonessential
68505 129 128 184 193 nonessential
69790 146 142 187 175 nonessential
69791 73 154 80 168 nonessential
69792 326 149 174 267 nonessential
69793 149 149 181 197 nonessential
1 304 277 319 240 unknown
2 115 96 139 235 unknown
3 433 371 565 428 unknown
4 65 169 147 68 unknown
5 44 19 69 73 unknown
6 228 339 131 173 unknown
7 430 268 428 278 unknown
8 268 272 278 221 unknown
9 143 87 163 93 unknown
10 218 200 209 189 unknown
11 289 57 172 219 unknown
12 158 158 98 236 unknown
13 308 302 342 290 unknown
14 195 152 357 43 unknown
15 357 378 366 529 unknown
16 571 179 464 130 unknown
17 387 105 360 384 unknown
18 364 379 511 341 unknown
19 269 102 67 90 unknown
20 241 184 342 343 unknown
21 482 542 472 411 unknown
22 229 192 165 287 unknown
23 123 100 43 53 unknown
24 268 291 333 127 unknown
25 172 138 143 159 unknown
26 103 220 180 35 unknown
27 157 170 149 51 unknown
28 126 156 109 206 unknown
29 140 286 175 182 unknown
30 648 431 481 286 unknown
31 52 50 136 13 unknown
32 231 161 358 120 unknown
33 199 120 231 211 unknown
34 264 144 244 497 unknown
35 287 259 178 172 unknown
36 324 254 397 351 unknown
37 81 66 76 49 unknown
38 114 12 25 17 unknown
39 276 127 274 252 unknown
40 190 137 211 84 unknown
41 190 187 175 94 unknown
42 289 239 523 473 unknown
43 231 180 133 145 unknown
44 191 150 185 60 unknown
45 338 181 203 180 unknown
46 394 402 313 258 unknown
47 278 121 241 253 unknown
48 16 52 69 11 unknown
49 521 306 556 369 unknown
50 471 504 301 420 unknown
51 251 264 255 330 unknown
52 122 173 398 243 unknown
53 233 334 314 354 unknown
54 192 162 225 76 unknown
55 194 216 165 84 unknown
56 182 131 314 151 unknown
57 515 170 457 166 unknown
58 249 150 133 319 unknown
59 144 128 298 197 unknown
60 150 207 448 105 unknown
can get bagel statistics sgrna-level
Code
get_bagel_statistics(data = test_classified_sgrna)
Message <simpleMessage>
Building BAGEL classification statistics...
Output
# A tibble: 10 x 17
sample max_essential max_nonessential max_unknown mean_essential
<chr> <dbl> <dbl> <dbl> <dbl>
1 T0_- 1182 915 931 343.
2 T18_A 314 793 925 50.2
3 T18_A_Starved 304 584 542 49.0
4 T18_B 294 636 761 43.6
5 T18_B_Starved 363 661 565 50.7
6 T18_C 205 665 648 42.8
7 T18_C_Starved 159 557 529 39.6
8 T3_A 360 492 431 113.
9 T3_B 249 328 354 80.1
10 T3_C 250 409 388 95.2
# i 12 more variables: mean_nonessential <dbl>, mean_unknown <dbl>,
# median_essential <dbl>, median_nonessential <dbl>, median_unknown <dbl>,
# min_essential <dbl>, min_nonessential <dbl>, min_unknown <dbl>,
# n_genes_essential <dbl>, n_genes_nonessential <dbl>, n_genes_unknown <dbl>,
# total_genes <dbl>
can get bagel statistics gene-level
Code
get_bagel_statistics(data = test_classified_gene, is_gene = T)
Message <simpleMessage>
Building BAGEL classification statistics...
Output
# A tibble: 10 x 17
sample max_essential max_nonessential max_unknown mean_essential
<chr> <dbl> <dbl> <dbl> <dbl>
1 T0_- 1182 915 931 343.
2 T18_A 314 793 925 50.2
3 T18_A_Starved 304 584 542 49.0
4 T18_B 294 636 761 43.6
5 T18_B_Starved 363 661 565 50.7
6 T18_C 205 665 648 42.8
7 T18_C_Starved 159 557 529 39.6
8 T3_A 360 492 431 113.
9 T3_B 249 328 354 80.1
10 T3_C 250 409 388 95.2
# i 12 more variables: mean_nonessential <dbl>, mean_unknown <dbl>,
# median_essential <dbl>, median_nonessential <dbl>, median_unknown <dbl>,
# min_essential <dbl>, min_nonessential <dbl>, min_unknown <dbl>,
# n_genes_essential <dbl>, n_genes_nonessential <dbl>, n_genes_unknown <dbl>,
# total_genes <dbl>
can get bagel statistics gene-level fold changes
Code
get_bagel_statistics(data = test_classified_fc_gene_narrow, is_gene = T, is_fc = T)
Message <simpleMessage>
Building BAGEL classification statistics...
Output
# A tibble: 3 x 19
sample NNMD Essential.Glass.Delta max_essential max_nonessential max_unknown
<chr> <chr> <chr> <dbl> <dbl> <dbl>
1 T3_A -2.502 2.553 -0.290 0.0318 -0.655
2 T3_B -2.430 4.084 -0.848 -0.732 -1.16
3 T3_C -1.807 3.606 -0.488 -0.486 -1.06
# i 13 more variables: mean_essential <dbl>, mean_nonessential <dbl>,
# mean_unknown <dbl>, median_essential <dbl>, median_nonessential <dbl>,
# median_unknown <dbl>, min_essential <dbl>, min_nonessential <dbl>,
# min_unknown <dbl>, n_genes_essential <dbl>, n_genes_nonessential <dbl>,
# n_genes_unknown <dbl>, total_genes <dbl>
can prepare essentiality data
Code
prepare_essentiality_data(data = test_avg_classified_fc_gene)
Output
$essentiality
ACTR10 BYSL CCDC84 CDCP2 CELA3A COPB1 CRX CST8 DEFB123 DOLK
1 1 1 0 0 1 0 0 0 1
ERCC2 EXOSC3 FAM47B GFM1 GJA8 GUCY2F HYPK IFNA5 IL9 MCM3
1 1 0 1 0 0 1 0 0 1
MFRP NCBP2 NOP56 NPHS2 OR10A2 OR10S1 PANX3 PDILT PPA1 RFC2
0 1 1 0 0 0 0 0 1 1
RPL12 RPL18 SNRPD2 TMEM207 UBE2N WDR25
1 1 1 0 1 1
$predictor
[1] -2.2014271 -1.8236720 -1.1793501 -0.8099540 -0.5105452 -2.7617258
[7] -0.7722082 -1.2019199 -1.9291828 -1.5892816 -1.8663399 -2.0399960
[13] -0.8658798 -1.3854727 -1.1666279 -1.5530624 -2.1071931 -0.4293259
[19] -1.4566546 -1.1754400 -1.4115151 -2.3198319 -2.1092655 -0.9654381
[25] -1.2053156 -0.9958179 -0.8259206 -1.3746929 -1.2871011 -2.7677641
[31] -4.7692111 -2.6629914 -1.9312815 -1.1161930 -0.5420802 -1.4475384
$min
[1] -4.769211
$modified_predictor
[1] 2.567784 2.945539 3.589861 3.959257 4.258666 2.007485 3.997003 3.567291
[9] 2.840028 3.179929 2.902871 2.729215 3.903331 3.383738 3.602583 3.216149
[17] 2.662018 4.339885 3.312557 3.593771 3.357696 2.449379 2.659946 3.803773
[25] 3.563895 3.773393 3.943291 3.394518 3.482110 2.001447 0.000000 2.106220
[33] 2.837930 3.653018 4.227131 3.321673
can process ROC
Code
process_roc(test_screen_roc, test_essentiality_data[["min"]])
Output
thresholds specificity sensitivity ppv
best_prec -1.930232 1 0.5263158 1
can plot ROC
Code
p$data
Output
FPR TPR
1 1.00000000 1.00000000
2 0.94117647 1.00000000
3 0.88235294 1.00000000
4 0.88235294 0.94736842
5 0.82352941 0.94736842
6 0.76470588 0.94736842
7 0.70588235 0.94736842
8 0.64705882 0.94736842
9 0.58823529 0.94736842
10 0.52941176 0.94736842
11 0.47058824 0.94736842
12 0.41176471 0.94736842
13 0.41176471 0.89473684
14 0.41176471 0.84210526
15 0.35294118 0.84210526
16 0.29411765 0.84210526
17 0.29411765 0.78947368
18 0.23529412 0.78947368
19 0.23529412 0.73684211
20 0.17647059 0.73684211
21 0.17647059 0.68421053
22 0.11764706 0.68421053
23 0.05882353 0.68421053
24 0.05882353 0.63157895
25 0.05882353 0.57894737
26 0.05882353 0.52631579
27 0.00000000 0.52631579
28 0.00000000 0.47368421
29 0.00000000 0.42105263
30 0.00000000 0.36842105
31 0.00000000 0.31578947
32 0.00000000 0.26315789
33 0.00000000 0.21052632
34 0.00000000 0.15789474
35 0.00000000 0.10526316
36 0.00000000 0.05263158
37 0.00000000 0.00000000
Code
p$layers
Output
[[1]]
geom_line: na.rm = FALSE, orientation = NA
stat_identity: na.rm = FALSE
position_identity
[[2]]
mapping: x = ~x, y = ~y
geom_text: na.rm = FALSE
stat_identity: na.rm = FALSE
position_identity
can average guide BFs
Code
average_guide_bfs(data = test_bf_matrix, gene_column = 1, data_columns = 2)
Output
# A tibble: 2 x 2
gene mean
<chr> <dbl>
1 ABCC3 -1.26
2 ABL1 -1.71
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