I am trying to perform methylation-gene expression correlation analysis in R.
After removing probes not mapped to any gene symbol, around 300000 probes remained.
Considering the large number of samples (280), the correlation analysis generates a huge adjacency matrix that it is impossible to be opened in excel.
Since there are several probes corresponding to each gene in methylation data, I have to perform all against all pairwise correlations and then filter out the results.
I searched for a way to filter out significant negative correlations, however after a couple of hours it is still running. I have already increased the memory of R using memory.limit() function.
Is there any way to do this task in my laptop (with 16G Ram) ? (I do not have any access to computer server right now)
I would appreciate any help