基于基因组区间的功能富集分析。
基本信息
| 软件包 | 链接 |
|---|---|
| 编程语言 | R, C++ |
| Bioconductor | https://bioconductor.org/packages/rGREAT/ |
| GitHub | https://github.com/jokergoo/rGREAT |
| 文档 | https://jokergoo.github.io/rGREAT/ |
| 论文 | Zuguang Gu, et al., rGREAT: an R/bioconductor package for functional enrichment on genomic regions. Bioinformatics 2023. |
例子
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 observed_region_hits
## 1 HALLMARK_PROTEIN_SECRETION 0.009545438 15
## 2 HALLMARK_FATTY_ACID_METABOLISM 0.011573276 17
## 3 HALLMARK_MTORC1_SIGNALING 0.016315292 21
## 4 HALLMARK_XENOBIOTIC_METABOLISM 0.013694524 17
## 5 HALLMARK_ADIPOGENESIS 0.014848629 18
## 6 HALLMARK_COAGULATION 0.010231163 12
## fold_enrichment p_value p_adjust mean_tss_dist observed_gene_hits
## 1 1.691530 0.03660128 0.9728496 169434 15
## 2 1.581164 0.04632617 0.9728496 167984 14
## 3 1.385507 0.08795227 0.9906854 285079 18
## 4 1.336246 0.14366715 0.9906854 220374 13
## 5 1.304880 0.15683279 0.9906854 262996 16
## 6 1.262527 0.24769378 0.9906854 206323 10
## gene_set_size fold_enrichment_hyper p_value_hyper p_adjust_hyper
## 1 95 2.0422886 0.006090193 0.2557881
## 2 157 1.1533944 0.328845663 0.9245430
## 3 200 1.1641045 0.284968109 0.9245430
## 4 197 0.8535453 0.762694041 0.9880034
## 5 200 1.0347596 0.481277540 0.9625551
## 6 136 0.9510658 0.612429803 0.9880034