I have the methylation data from human methylation450k. Now I am trying to calculate the distance between CpG site and TSS. I need all the possible association between gene and CpG, as well the nearest gene. Is there a way to do this fast?
You could GALAXY which is a simple to use graphical interface for using bioinformatic tools. If your files contain chromosome, start and end coordinates you can find the closest TSS to each CpG (using 'Fetch closest non-overlapping feature') and then calculate the distance (using the 'compute' tool).
I advise following along with the Galaxy101 tutorial to get yourself familiar with the layout.