Gene ontology enrichment using FUNC
GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (Homo.sapiens by default); the GO-graph is included in the package and updated regularly. GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests:
the Wilcoxon rank-sum test that is used when genes are ranked,
a binomial test that is used when genes are associated with two counts, and
a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts.
To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.
| System | Target | Derivation | Build status |
|---|---|---|---|
| x86_64-linux | /gnu/store/ql9zzn09yyxbyskb64lxgxhvb26nzma0-r-gofuncr-1.16.0.drv | ||
| riscv64-linux | /gnu/store/1aw6zmc5xrxd512hg6k9297h86min45h-r-gofuncr-1.16.0.drv | ||
| powerpc-linux | /gnu/store/srnsnlj1qwcnpswy205ksrxi25nslwzn-r-gofuncr-1.16.0.drv | ||
| powerpc64le-linux | /gnu/store/45rhbcldb65yhxngs2qai6krdhdk0r7m-r-gofuncr-1.16.0.drv | ||
| mips64el-linux | /gnu/store/xq5hb27d34jxpvhvnbsrd229iz6hd6sd-r-gofuncr-1.16.0.drv | ||
| i686-linux | /gnu/store/rf3rvlv7ya229h8wj89nvzr1d91jfg3q-r-gofuncr-1.16.0.drv | ||
| i586-gnu | /gnu/store/frra3a8qdn5pl4pv1642fnw1a7ps7270-r-gofuncr-1.16.0.drv | ||
| armhf-linux | /gnu/store/h173df87xfgdaych7wwgm0anxf2n9kln-r-gofuncr-1.16.0.drv | ||
| aarch64-linux | /gnu/store/z1z0zqk3kdqx1sl94if349frm7r7b7k4-r-gofuncr-1.16.0.drv |
| Linter | Message | Location |
|---|---|---|
| No lint warnings ✓ | ||