In order to do test analysis of DNA methylation data I need to cluster the data based on 27 markers described in Shen, 2007. Seven out of those markers are MINTs and I need to figure out what would be their most likely location on the 450k array. I will use Bioconductor IlluminaHumanMethylation450k.db package for annotation (i.e. chromosome and location of the probes) but some of the features are confusing. Here I test what each annotation feature in the package really means.
IlluminaHumanMethylation450kCHR36: What chromosome does the target sequence for a probe align to, in build 36
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IlluminaHumanMethylation450kCHRLOC: IlluminaHumanMethylation450kCHRLOC is an R object that maps manufacturer identifiers to the starting position of the gene. The position of a gene is measured as the number of base pairs. The CHRLOCEND mapping is the same as the CHRLOC mapping except that it specifies the ending base of a gene instead of the start. Each manufacturer identifier maps to a named vector of chromosomal locations, where the name indicates the chromosome. Due to inconsistencies that may exist at the time the object was built, these vectors may contain more than one chromosome and/or location. If the chromosomal location is unknown, the vector will contain an NA. Chromosomal locations on both the sense and antisense strands are measured as the number of base pairs from the p (5’ end of the sense strand) to q (3’ end of the sense strand) arms. Chromosomal locations on the antisense strand have a leading "-" sign (e. g. -1234567). Since some genes have multiple start sites, this field can map to multiple locations. Mappings were based on data provided by: UCSC Genome Bioinformatics (Homo sapiens) ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19 With a date stamp from the source of: 2010-Mar22
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> x <- IlluminaHumanMethylation450kCHRLOC
> xx <- as.list(x)[1:3]
> xx
$cg00000029
16
53468350
$cg00000108
3 3
37440967 37440967
$cg00000109
3 3
171757417 171758343 |
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