I have just started an internship in bioinformatic and I have to deal with big data from Hi-C. I want to analyze my data with R.
The data looks like this:---> chrom start end count
I want to build a matrix where each bins fills with the count. And after, select significant interactions and (if it is possible) to plot the heat map.
It works for low resolution (500kb,100kb), but when I try to run my code with high resolution (10kb, 5kb), problems occurs and R doesn't want to compute with big data.
So I try to use a sparse matrix but I can't process all my code with this, I have to transform into an matrix.
So if you have a solution and you have already managed this kind of problem, let me know.
If you have a method to find significant interactions with high resolution, it will be great. =)
Thank you very much,