Fig. 6From: GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorizationEvaluating the benefits of smoothing in GRiNCH. Recovery of topology and significant interactions from downsampled then smoothed data. A Rand index and mutual information were used to measure the similarity between TADs from high-depth GM12878 dataset and TADs from downsampled datasets smoothed by different methods (GRiNCH, Mean Filter, Gaussian Filter, HiCNN). Directionality was used as a TAD-calling method independent of any of the smoothing methods, i.e., GRiNCH. The mean is computed across chromosomes and the error bar denotes deviation from the mean. B Area under precision-recall curve (AUPR) was used to measure the recovery of significant interactions called by Fit-Hi-C. Precision and recall were measured for significant interactions from downsampled and smoothed datasets against the “ground truth” defined by the significant interactions from the high-depth GM12878 dataset. Since the pretrained HiCNN models imputes interactions up to 2MB apart, the AUPR for interactions <2MB apart and for all interactions are shown hereBack to article page