How to get illumina CpG IDs by gene name?
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@d-16116
Last seen 5 weeks ago
UK

Hi all,

Hopefully a simple one. I have used Rnbeads to generate M values for some 450k arrays, can happily export the site level data by cg ID and gene/promoter level data too. However, I can't find a simple within R way of generating a list of cg IDs by gene?

                    Chromosome   Start     End Strand     symbol                      entrezID  CpG    GC     C     G
ENSG00000227232       chr1   14363   29806      -     WASH7P              653635;100287171  380  8441  4320  4121
ENSG00000186092       chr1   69091   70008      +      OR4F5                         79501   11   393   218   175
ENSG00000237683       chr1  134901  139379      -       <NA>    728728;100996768;101929819  181  2886  1113  1773
ENSG00000268903       chr1  135141  135895      -       <NA>                          <NA>   42   511   198   313
ENSG00000237094       chr1  317720  453948      +       <NA> 101928706;101929822;101929823 1498 57740 28840 28900
ENSG00000239664       chr1  529833  532878      -       <NA>                          <NA>   60  1371   850   521

I can intersect the coordinates manually, but is there a simple way of exporting the CpG IDs by gene? i.e. the 380 CpGs present in ENSG00000227232. - which CpGs are they?

And going the opposite way, given a list of CpG IDs (e.g. cg13869341, cg14008030, cg12045430), which package/function will tell me what genes they are in without me needing to intersect them manually?

Thanks in advance!

MethylationArrayData RnBeads • 67 views
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