Fig. 3
From: Effective normalization for copy number variation in Hi-C data
Generalization of matrix balancing algorithms for cancer Hi-C data. a. Rationale of LOIC method versus standard ICE method. The LOIC method extends the ICE normalization by constraining the genome-wide Hi-C 1D profile to follow the copy number signal. b. Segmentation of the Hi-C 1D genome-wide profile of simulated cancer data. The red line represents the smoothing line that estimate the copy number level. c. LOIC normalized Hi-C contact maps of simulated data on the first four chromosomes. The 1D profiles are represented by the sum of genome-wide contacts at each locus using either all (inter and intra-chromosomal), cis (intra-chromosomal) or trans (inter-chromosomal) contacts. As a results, we can see that the LOIC method allows to normalize cancer Hi-C data keeping into account the copy number information