Hi,
Just recently I got my first EPIC array results and I am not really experienced with RnBeads.
1.) I got the diffMethTable for sites, genes and promoters. The annotation of genes and promoters is quite clear, but some sites (cg...) are also close to a gene, or within. Can the site table be annotated with genes, since the chr and start/end are also given in the table? Then it would be easier to search for all cgs located in the eg. IL4 gene. This is important for me to identify cgs in specific genes and design further DNA Methylation assays on our PyroMark instrument.
2.) Next, I have several genes of interest which are differentially methylated. Currently, I was not able to find a way to plot the mean beta values of the compared groups of the diffMethTable in a e.g. box plot. How can I extract them and plot these values?
3.) I did a GO term analysis and wanted to plot the results of the GOHyperGResult class with termGraph, inducedTermGraph and plotTermGraph. Does anybody have experiences with that and can help me? With my normal analyses of ChIP data I use ChIPseeker and with this R package it is quite easy and straight forward to get GO enrichment plots.
Many thanks for your help! Angelika
