Hello everyone,
I am new to this forum so I'm apologizing in advance if I am not posting in the most formal way.
I am using the goseq package from bioconductor in order to perform enrichment for markers that are differentially methylated (limma output). These markers have been measured according to CpG arrays from 450K illumina (i.e. cg07790169) and I am retrieving them on ucsc website. I am a newbie at using the goseq library, so I do not know it in details. But my understanding is that it uses codes from Ensembl (i.e. ENSG00....) and not gene codes from UCSC.
Therefore, I would like to know whether there is a package that would allow to link in a very straightforward way a methylation marker (i.e. cg07790169) to an Ensembl gene code (i.e. ENSG00...) so that I could properly run goseq.
I could do it by copy and paste, but it would be extremely time consuming (I have several hundred methylation markers).
Thank you for your kind help and understanding
And re: required reading, I would recommend the help pages for the FDb.InfiniumMethylation.hg19 package, particularly the
getNearest
function, which should be relevant.James, there is some literature on using goseq for DNA methylation data, and there is in fact a Bioconductor package called 'missMethyl' which has a function called 'gometh' which was specifically developed to apply goseq methods to the illumina 450k platform. The idea being that genes with differing # of CpGs are a priori more/less likely to appear in the DMR gene set, so gometh would help correct for that bias.
References:
Gene-set analysis is severely biased when applied to genome-wide methylation data
https://academic.oup.com/bioinformatics/article/29/15/1851/265573
missMethyl
https://bioconductor.org/packages/release/bioc/html/missMethyl.html
Sure. But that corrects for the fact that there may be more or less CpGs on an Illumina array that are sufficiently close to a given gene, which may or may not have anything to do with the length of the gene, which is what goseq is concerned with. Or do I miss something?