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Table 3 Similarity between A/B compartments detected following various normalization methods

From: HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

Comparison

Mean Absolute Correlation

Mean Percentage

Jaccard A

Jaccard B

Loess vs. Raw

0.9954

0.8537

0.7971

0.7823

MA vs. Raw

0.9950

0.8539

0.7881

0.7706

ICE vs. Raw

0.9795

0.7850

0.6731

0.6277

KR vs. Raw

0.9489

0.7771

0.5945

0.5000

SCN vs. Raw

0.9309

0.8083

0.6134

0.5495

ChromoR vs. Raw

0.8093

0.6810

0.5210

0.4803

  1. “Correlation” - Pearson correlation coefficient between principal components defining A/B compartments in raw vs. normalized Hi-C data; “Prop. Match Sign” - the proportion of regions with matching signs defining A/B compartments; “Jaccard A/B” - Jaccard overlap statistics between A/B compartments, respectively. All values represent averages over all chromosomes
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BMC Bioinformatics

ISSN: 1471-2105

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