keyword_enrichment_from_GO.RdKeyword enrichment for GO terms
keyword_enrichment_from_GO(go_id, min_bg = 5, min_term = 2)A vector of GO IDs.
Minimal number of GO terms (in the background, i.e. all GO temrs in the GO database) that contain a specific keyword.
Minimal number of GO terms (GO terms in go_id) that contain a specific keyword.
The enrichment is applied by Fisher's exact test. For a keyword, there is the following 2x2 contigency table:
| contains the keyword | does not contain the keyword
In the GO set | s11 | s12
Not in the GO set | s21 | s22 where s11, s12, s21 and s22 are number of GO terms in each category.
A data frame with keyword enrichment results.
# \dontrun{
go_id = random_GO(100)
keyword_enrichment_from_GO(go_id)
#> keyword n_term n_bg p padj
#> 1 positive 21 3338 1.610552e-05 0.0008858037
#> 2 regulation 42 10445 3.913273e-05 0.0021131673
#> 3 acetylation 3 102 1.652342e-03 0.0875741136
#> 4 synaptic 4 233 2.005367e-03 0.1042790660
#> 5 vascular 3 116 2.383949e-03 0.1215813808
#> 6 telomeric 2 48 5.368536e-03 0.2684267755
#> 7 meiosis 2 63 9.092313e-03 0.4455233527
#> 8 glucose 2 83 1.538534e-02 0.7384961011
#> 9 transmission 2 96 2.022839e-02 0.9507342165
#> 10 proteincoupled 2 116 2.873885e-02 1.0000000000
#> 11 negative 13 3274 3.387229e-02 1.0000000000
#> 12 endosome 2 127 3.392720e-02 1.0000000000
#> 13 disassembly 2 133 3.689944e-02 1.0000000000
#> 14 phosphorylation 2 137 3.893466e-02 1.0000000000
#> 15 histone 3 344 4.377305e-02 1.0000000000
#> 16 initiation 2 147 4.420400e-02 1.0000000000
#> 17 stress 2 162 5.256851e-02 1.0000000000
#> 18 muscle 4 623 5.372262e-02 1.0000000000
#> 19 smooth 2 185 6.637452e-02 1.0000000000
#> 20 assembly 4 746 9.013424e-02 1.0000000000
#> 21 viral 2 227 9.420181e-02 1.0000000000
#> 22 via 3 513 1.114850e-01 1.0000000000
#> 23 cycle 2 259 1.172488e-01 1.0000000000
#> 24 processing 2 279 1.323016e-01 1.0000000000
#> 25 cell 12 3738 1.397014e-01 1.0000000000
#> 26 interleukin 2 294 1.438659e-01 1.0000000000
#> 27 activation 2 298 1.469853e-01 1.0000000000
#> 28 protein 6 1623 1.635079e-01 1.0000000000
#> 29 transport 5 1291 1.700122e-01 1.0000000000
#> 30 vesicle 2 359 1.960134e-01 1.0000000000
#> 31 response 7 2112 2.034871e-01 1.0000000000
#> 32 polymerase 2 372 2.067285e-01 1.0000000000
#> 33 ii 2 373 2.075555e-01 1.0000000000
#> 34 metabolic 6 1787 2.199560e-01 1.0000000000
#> 35 migration 2 389 2.208330e-01 1.0000000000
#> 36 secretion 2 410 2.383628e-01 1.0000000000
#> 37 organization 2 419 2.459004e-01 1.0000000000
#> 38 catabolic 5 1547 2.744703e-01 1.0000000000
#> 39 transcription 2 475 2.928899e-01 1.0000000000
#> 40 ion 2 526 3.353872e-01 1.0000000000
#> 41 growth 2 545 3.510498e-01 1.0000000000
#> 42 cellular 3 932 3.545236e-01 1.0000000000
#> 43 factor 2 554 3.584270e-01 1.0000000000
#> 44 rna 2 614 4.067680e-01 1.0000000000
#> 45 dna 2 687 4.631534e-01 1.0000000000
#> 46 receptor 4 1561 4.743773e-01 1.0000000000
#> 47 membrane 3 1219 5.249771e-01 1.0000000000
#> 48 morphogenesis 2 798 5.426343e-01 1.0000000000
#> 49 pathway 3 1287 5.618735e-01 1.0000000000
#> 50 process 13 5825 5.696686e-01 1.0000000000
#> 51 involved 4 1850 6.089469e-01 1.0000000000
#> 52 differentiation 2 933 6.279394e-01 1.0000000000
#> 53 signaling 3 1429 6.331736e-01 1.0000000000
#> 54 development 3 1455 6.453391e-01 1.0000000000
#> 55 activity 2 10285 1.000000e+00 1.0000000000
# }