Fig. 3
From: HiCHap: a package to correct and analyze the diploid Hi-C data
Evaluation of SNP-bias correction in HiCHap. (a) Examples showing the improved quality of HiCHap contact maps. Circles denote the called chromatin loop, and dashed rectangles show the map differences in local regions between HiCHap contact maps and SNP-biased contact maps. (b) Genome-wide evaluations (* 0.01 ≤ p < 0.05, ** p < 0.01). The boxplots are drawn by combining maternal and paternal PCCs. In cell type E7.5, the PC2 is selected for five chromosomes and the PC1 is selected for the rest chromosomes in HiCHap contact maps, whereas the PC2 is selected for all chromosomes in SNP-biased contact maps