Functional enrichment analysis on genomic regions.
Basic
| 软件包 | 链接 |
|---|---|
| Language | R, C++ |
| Bioconductor | https://bioconductor.org/packages/rGREAT/ |
| GitHub | https://github.com/jokergoo/rGREAT |
| Documentation | https://jokergoo.github.io/rGREAT/ |
| Publication | Zuguang Gu, et al., rGREAT: an R/bioconductor package for functional enrichment on genomic regions. Bioinformatics 2023. |
Example
library(rGREAT)
gr = randomRegions(nr = 1000, genome = "hg19")
res = great(gr, "MSigDB:H", "TxDb.Hsapiens.UCSC.hg19.knownGene")
tb = getEnrichmentTable(res)
head(tb)
## id genome_fraction
## 1 HALLMARK_ESTROGEN_RESPONSE_LATE 0.019761793
## 2 HALLMARK_TGF_BETA_SIGNALING 0.007140288
## 3 HALLMARK_ESTROGEN_RESPONSE_EARLY 0.024463198
## 4 HALLMARK_PROTEIN_SECRETION 0.009545438
## 5 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.030187448
## 6 HALLMARK_INFLAMMATORY_RESPONSE 0.021400596
## observed_region_hits fold_enrichment p_value p_adjust mean_tss_dist
## 1 29 1.584750 0.01179918 0.3992542 254762
## 2 13 1.966150 0.01774463 0.3992542 249538
## 3 31 1.368477 0.05274030 0.7323745 238970
## 4 14 1.583876 0.06509996 0.7323745 149002
## 5 35 1.252076 0.10694419 0.9609538 240512
## 6 25 1.261546 0.14432481 0.9609538 229830
## observed_gene_hits gene_set_size fold_enrichment_hyper p_value_hyper
## 1 25 198 1.633143 0.0103653538
## 2 11 54 2.634804 0.0024570576
## 3 26 198 1.698469 0.0054923334
## 4 13 95 1.769983 0.0308609265
## 5 31 199 2.014921 0.0001401821
## 6 23 197 1.510119 0.0310192081
## p_adjust_hyper
## 1 0.116610230
## 2 0.055283797
## 3 0.082385001
## 4 0.232644061
## 5 0.006308193
## 6 0.232644061