missMethyl - get names of differentially methylated genes from gometh()
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stewart999 ▴ 10
Last seen 6 months ago
United Kingdom

I'm using the gometh() function of missMethyl and am trying to pull out the names of the differentially methylated genes from the output table, which looks like this:

go <- missMethyl::gometh(sig.cpg=sig.cpg, all.cpg=all.cpg, array.type="EPIC", collection="GO")
           ID   ONT                                             TERM   N DE         P.DE          FDR
1: GO:0015748    BP                  organophosphate ester transport 116  5 4.907299e-08 0.0002769925
2: GO:0015914    BP                           phospholipid transport  90  5 1.505420e-08 0.0002769925
3: GO:0034382    BP                    chylomicron remnant clearance   9  3 3.849721e-08 0.0002769925
4: GO:0071830    BP triglyceride-rich lipoprotein particle clearance   9  3 3.849721e-08 0.0002769925
5: GO:0033700    BP                              phospholipid efflux  12  3 6.832103e-08 0.0003085104
6: GO:0008203    BP                    cholesterol metabolic process 146  5 1.082826e-07 0.0003628179

The DE column is the number of genes that are differentially methylated. How do I find out, for example, the names of the 5 differentially methylated genes for GO:0015748?

Thanks, Stewart

missMethyl • 254 views
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Last seen 10 months ago

Hi Stewart,

We recently implemented a parameter in gometh, sig.genes, allowing you to output an extra column in the results table showing the genes in the gene set that overlap the DM CpGs. It is set to FALSE by default.

Ensure that you have the latest version of missMethyl installed to be able to use it.

Cheers, Jovana


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