I have downloaded 56G data from ICGC and I am having trouble analyzing it on R (Although I have access to a server). I know that ICGC data is stored in GDC. However, to analyze big data on R, I see suggestions like using SQL through dplyr/R.
Do you know any way to do that? And I would like to know how do you work with big data from databases such as ICGC and TCGA when you need to use R.
I downloaded methylation data for 269 donors
meth_array.PACA-AU.tsv.gz from here using wget:
I want to compare mean methylation level of selected cg probes across patients.
I would appreciate any help!