This reference stores a number of useful region set annotations to be used in RnBeads analyses. You can find a list of available region sets along with their descriptions below. Here is an example showing how you can employ them in your analyses:
REGION_SET <- "tiling1kb"
ASSEMBLY <- "hg19"
rnb.load.annotation.from.db(REGION_SET, assembly=ASSEMBLY)
rnb.options(region.types=union(rnb.getOption("region.types"), REGION_SET))
| Region Set | Assembly | File | N | Description |
|---|---|---|---|---|
| tiling | hg19 | [native] | 619146 | Genome tiling regions of length 5000 |
| genes | hg19 | [native] | 57736 | Ensembl genes, version Ensembl Genes 75 |
| promoters | hg19 | [native] | 57736 | Promoter regions of Ensembl genes, version Ensembl Genes 75 |
| cpgislands | hg19 | [native] | 27718 | CpG island track of the UCSC Genome browser |
| tiling200bp | hg19 | download | 15478399 | Genome tiling regions using a window size of 200bp |
| tiling500bp | hg19 | download | 6191368 | Genome tiling regions using a window size of 500bp |
| tiling1kb | hg19 | download | 3095689 | Genome tiling regions using a window size of 1kb |
| tiling10kb | hg19 | download | 309579 | Genome tiling regions using a window size of 10kb |
| ensembleRegBuildBPall | hg19 | download | 613343 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- all |
| ensembleRegBuildBPctcf | hg19 | download | 78648 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- ctcf |
| ensembleRegBuildBPdistal | hg19 | download | 169651 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- distal |
| ensembleRegBuildBPdnase | hg19 | download | 51267 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- dnase |
| ensembleRegBuildBPproximal | hg19 | download | 146789 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- proximal |
| ensembleRegBuildBPtfbs | hg19 | download | 141385 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- tfbs |
| ensembleRegBuildBPtss | hg19 | download | 25603 | Ensembl Regulatory build from BLUEPRINT data release 20150128 -- tss |
| deepGC19promoters | hg19 | download | 57783 | DEEP reference genes derived from Gencode 19 gene annotations. Promotor annotation. Promoters are defined as 1500 bp upstream to 500 downstream of the TSS. |
| deepGC19genes | hg19 | download | 57783 | DEEP reference genes derived from Gencode 19 gene annotations. Gene annotation. |
| dynamicMethZiller2013 | hg19 | download | 716087 | Dynamically methylated regions extracted from Ziller, et al. (2013). Nature, 500(7463), 477â481. http://doi.org/10.1038/nature12433. Assembly: hg19 |
| tiling | hg38 | [native] | 617665 | Genome tiling regions of length 5000 |
| genes | hg38 | [native] | 60070 | Ensembl genes, version Ensembl Genes 78 |
| promoters | hg38 | [native] | 60070 | Promoter regions of Ensembl genes, version Ensembl Genes 78 |
| cpgislands | hg38 | [native] | 27949 | CpG island track of the UCSC Genome browser |
| tiling200bp | hg38 | download | 15441361 | Genome tiling regions using a window size of 200bp |
| tiling500bp | hg38 | download | 6176550 | Genome tiling regions using a window size of 500bp |
| tiling1kb | hg38 | download | 3088281 | Genome tiling regions using a window size of 1kb |
| tiling10kb | hg38 | download | 308837 | Genome tiling regions using a window size of 10kb |
| ensembleRegBuildBPall | hg38 | download | 528248 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- all |
| ensembleRegBuildBPctcf | hg38 | download | 116838 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- ctcf |
| ensembleRegBuildBPdistal | hg38 | download | 197516 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- distal |
| ensembleRegBuildBPdnase | hg38 | download | 54016 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- dnase |
| ensembleRegBuildBPproximal | hg38 | download | 95397 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- proximal |
| ensembleRegBuildBPtfbs | hg38 | download | 40751 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- tfbs |
| ensembleRegBuildBPtss | hg38 | download | 23730 | Ensembl Regulatory build from BLUEPRINT data release 20150820 -- tss |
| gencode22promoters | hg38 | download | 60446 | Reference annotation derived from Gencode 22 gene annotations. Gene annotation. Promotor annotation. Promoters are defined as 1500 bp upstream to 500 downstream of the TSS. |
| gencode22genes | hg38 | download | 60446 | Reference annotation derived from Gencode 22 gene annotations. Gene annotation. |
| dynamicMethZiller2013 | hg38 | download | 716087 | Dynamically methylated regions extracted from Ziller, et al. (2013). Nature, 500(7463), 477â481. http://doi.org/10.1038/nature12433. Assembly: hg38. liftOver from hg19. |
| tiling | mm9 | [native] | 530988 | Genome tiling regions of length 5000 |
| genes | mm9 | [native] | 37583 | Ensembl genes, version Ensembl Genes 67 |
| promoters | mm9 | [native] | 37583 | Promoter regions of Ensembl genes, version Ensembl Genes 67 |
| cpgislands | mm9 | [native] | 15991 | CpG island track of the UCSC Genome browser |
| tiling200bp | mm9 | download | 13274487 | Genome tiling regions using a window size of 200bp |
| tiling500bp | mm9 | download | 5309802 | Genome tiling regions using a window size of 500bp |
| tiling1kb | mm9 | download | 2654907 | Genome tiling regions using a window size of 1kb |
| tiling10kb | mm9 | download | 265500 | Genome tiling regions using a window size of 10kb |
| tiling | mm10 | [native] | 545114 | Genome tiling regions of length 5000 |
| genes | mm10 | [native] | 43309 | Ensembl genes, version ENSEMBL GENES 79 (SANGER UK) |
| promoters | mm10 | [native] | 43309 | Promoter regions of Ensembl genes, version ENSEMBL GENES 79 (SANGER UK) |
| cpgislands | mm10 | [native] | 16009 | CpG island track of the UCSC Genome browser |
| tiling200bp | mm10 | download | 13627618 | Genome tiling regions using a window size of 200bp |
| tiling500bp | mm10 | download | 5451055 | Genome tiling regions using a window size of 500bp |
| tiling1kb | mm10 | download | 2725532 | Genome tiling regions using a window size of 1kb |
| tiling10kb | mm10 | download | 272564 | Genome tiling regions using a window size of 10kb |