Output coordinates question

Question

Output coordinates question

Closed this issue 6 years ago · 4 comments

Hi, thank you very much for this tool, I have tried to use it and was pleasantly surprised - very easy to use and fast!

I however have a small question about the output coordinates of pyHICCUPS. What do they correspond to? What is the difference between loc_1 and centroid_x? Sometimes they are the same, and sometimes they are not... And how is radius determined?

Thank you,
Ilya

Answer 1 · 2018-10-26T12:20:57.000Z

Basically, what is the correct way to convert the output to bedpe for visualization in e.g. HiGlass?

Answer 2 · 2018-10-29T21:02:17.000Z

Hello, use loc_1 and loc_2 instead of centroid_x and centroid_y in post analysis and visualization, because (loc_1, loc_2) corresponds to the peak with the greatest interaction frequency in each cluster, while (centroid_x, centroid_y) just indicates the cluster centroid.

Answer 3 · 2018-10-29T21:11:27.000Z

pyHICCUPS implements the greedy clustering algorithm proposed by the original paper (Rao et al. Cell. 2014), and the radius is defined as the Euclidean distance between the centroid of a cluster and the furthest peak pixel in the same cluster.

Answer 4 · 2018-10-30T11:01:29.000Z

Thank you very much for the explanation!