Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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Yveto • 0
@104a8f13
Last seen 5 months ago
Canada

Hi, I'm a beginner with Bioconductor packages. I have a data frame (365000*355) with beta mesures of dna methylation. The dimnames of my data are CpG names on lines and ids on colonnes. So I extract the names of CpG sites (ex : "cg00000029" "cg00000109" "cg00000165" "cg00000236" "cg00000289") and I would like to get their genomic coordinates in R. If I search the CpG's name on UCSC Genome Browser on Human (GRCh37/hg19), I can get the name of Chromosome and the genomic position( Example cg00000029 : chromosome ch16; genomic position 53,468,112). But I cannot search manually all the CpG's genomic coordinates on the UCSC Genome Browser on Human (GRCh37/hg19). I will take too long. Do you know a R function of bioconductor package that I can use to solve my problem? Thank you very much. Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData • 1.0k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

You don't say what array that is, so I will guess.

> library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
> Locations
DataFrame with 865859 rows and 3 columns
                   chr       pos      strand
           <character> <integer> <character>
cg18478105       chr20  61847650           -
cg09835024        chrX  24072640           -
cg14361672        chr9 131463936           +
cg01763666       chr17  80159506           +
cg12950382       chr14 105176736           +
...                ...       ...         ...
cg23079522        chr3 160569628           -
cg16818145        chr3 182782277           -
cg14585103        chr8 139940608           -
cg10633746       chr17  18164442           +
cg12623625        chr1  17946923           +
>
0
Entering edit mode

Thank for your response. It is Illumina 450 K. I use this code

```{r }

library(IlluminaHumanMethylation450kanno.ilmn12.hg19)

annotation <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)

```

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