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Table 1 Evaluation of the effect of normalization on differential chromatin interaction detection

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

Fold change

HiCcompare

MA

ICE

SCN

KR

ChromoR

2

0.847

0.823

0.835

0.768

0.748

0.149

3

0.973

0.934

0.802

0.721

0.764

0.380

4

0.995

0.98

0.953

0.881

0.868

0.532

  1. Matthews Correlation Coefficient of detecting 200 controlled differences in jointly (HiCcompare) vs. individually normalized Gm12878 datasets, chromosome 1, 1 MB resolution. Matrices were normalized with methods corresponding to column labels; differences were detected using HiCcompare
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BMC Bioinformatics

ISSN: 1471-2105

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