Region Set Resource

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), 477–481. 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), 477–481. 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