IlluminaHumanMethylationEPICv2anno.20a2.hg38.RdThis package is based on the file https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/methylationepic/InfiniumMethylationEPICv2.0ProductFiles(ZIPFormat).zip from https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html.
Additional SNP annotation is generated by the authors (described in SNPs.CommonSingle).
A script for creating the data object in this package is contained in
scripts/createAnno.R.
An object of class IlluminaMethylationAnnotation for
IlluminaHumanMethylationEPIv2Canno.20a2.hg38. All others are of
class DataFrame
The following changes/ modifications / addition has been made to the source material.
For the annotation related to UCSC islands, a value of "" has
been changed to "OpenSea".
The creation of this object based on the Illumina annotation and
additional SNP information (see SNPs.CommonSingle) is contained in the
createAnno.R script in the scripts directory.
Contents of the columns are the responsibility of Illumina; see their documentation for details.
See description.
IlluminaHumanMethylationEPICv2anno.20a2.hg38
#> IlluminaMethylationAnnotation object
#> Annotation
#> array: IlluminaHumanMethylationEPICv2
#> annotation: 20a2
#> genomeBuild: hg38
#> Available annotation
#> Islands.UCSC
#> Locations
#> Manifest
#> Other
#> SNPs.141CommonSingle
#> SNPs.142CommonSingle
#> SNPs.144CommonSingle
#> SNPs.146CommonSingle
#> SNPs.147CommonSingle
#> SNPs.150CommonSingle
#> SNPs.151CommonSingle
#> SNPs.Illumina
#> Defaults
#> Locations
#> Manifest
#> SNPs.151CommonSingle
#> Islands.UCSC
#> Other
Locations
#> DataFrame with 930075 rows and 3 columns
#> chr pos strand
#> <character> <integer> <character>
#> cg25324105_BC11 chr19 37692358 +
#> cg25383568_TC11 chr19 38727081 -
#> cg25455143_BC11 chr19 1591515 -
#> cg25459778_BC11 chr16 1614581 +
#> cg25487775_BC11 chr2 161237458 +
#> ... ... ... ...
#> ch.22.16108507R_BC21 chr22 17247617 +
#> ch.22.40657F_BC21 chr22 17685590 -
#> ch.22.78028F_BC21 chr22 19374531 -
#> ch.22.17803970R_BC21 chr22 19436447 +
#> ch.22.107403R_TC21 chr22 20144102 +
Manifest
#> DataFrame with 930075 rows and 8 columns
#> Name AddressA AddressB
#> <character> <character> <character>
#> cg25324105_BC11 cg25324105_BC11 1754126 99753217
#> cg25383568_TC11 cg25383568_TC11 79792482 69667133
#> cg25455143_BC11 cg25455143_BC11 80699190 7659147
#> cg25459778_BC11 cg25459778_BC11 60797262 65710482
#> cg25487775_BC11 cg25487775_BC11 5799427 89606481
#> ... ... ... ...
#> ch.22.16108507R_BC21 ch.22.16108507R_BC21 88698463
#> ch.22.40657F_BC21 ch.22.40657F_BC21 51795249
#> ch.22.78028F_BC21 ch.22.78028F_BC21 43681841
#> ch.22.17803970R_BC21 ch.22.17803970R_BC21 17741188
#> ch.22.107403R_TC21 ch.22.107403R_TC21 89738435
#> ProbeSeqA ProbeSeqB Type
#> <character> <character> <character>
#> cg25324105_BC11 ATTTATAAACTAATAACCCA.. GTTTATAAACTAATAACCCG.. I
#> cg25383568_TC11 AAACCAAAAAAATAACAAAC.. AAACCGAAAAAATAACAAAC.. I
#> cg25455143_BC11 ATAAAAAAAAATATACAACT.. ATAAAAAAAAATATACGACT.. I
#> cg25459778_BC11 AAAAATTTAAAACAAACAAC.. AAAAATTTAAAACAAACAAC.. I
#> cg25487775_BC11 AAAAACAACCTAAAAAACAA.. AAAAACAACCTAAAAAACAA.. I
#> ... ... ... ...
#> ch.22.16108507R_BC21 CTATTCTTTTTACTTAAACA.. II
#> ch.22.40657F_BC21 AATAAATAAACAAAATATAA.. II
#> ch.22.78028F_BC21 ACAATTCCTAAAAACTAACA.. II
#> ch.22.17803970R_BC21 CAACCAAAATTAAAATTAAT.. II
#> ch.22.107403R_TC21 CTTTCTCTTTAAAACCAATA.. II
#> NextBase Color
#> <character> <character>
#> cg25324105_BC11 A Red
#> cg25383568_TC11 C Grn
#> cg25455143_BC11 T Red
#> cg25459778_BC11 C Grn
#> cg25487775_BC11 A Red
#> ... ... ...
#> ch.22.16108507R_BC21
#> ch.22.40657F_BC21
#> ch.22.78028F_BC21
#> ch.22.17803970R_BC21
#> ch.22.107403R_TC21
data(SNPs.Illumina) # data object too large, need to be loaded manually by data()
Islands.UCSC
#> DataFrame with 930075 rows and 2 columns
#> Islands_Name Relation_to_Island
#> <character> <character>
#> cg25324105_BC11 chr19:37691892-37692.. Island
#> cg25383568_TC11 chr19:38726890-38727.. Island
#> cg25455143_BC11 chr19:1591428-159162.. Island
#> cg25459778_BC11 chr16:1610053-1615094 Island
#> cg25487775_BC11 chr2:161237949-16123.. Shore
#> ... ... ...
#> ch.22.16108507R_BC21 OpenSea
#> ch.22.40657F_BC21 OpenSea
#> ch.22.78028F_BC21 OpenSea
#> ch.22.17803970R_BC21 chr22:19431718-19432.. Shelf
#> ch.22.107403R_TC21 chr22:20142873-20143.. Shore
data(Other) # data object too large, need to be loaded manually by data()