Table 2 Numbers of significant proximal HVRs identified by applying different parameter estimation methods with various cutoffs of the BH-adjusted p-value. The original method refers to the moment matching method used by MAnorm2, and the other method corresponds to the default settings of HyperChIP
From: HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples
Parameter estimation | Data set | Number of significant proximal HVRs | ||
|---|---|---|---|---|
0.01 | 0.05 | 0.1 | ||
Original | H3K27ac ChIP-seq | 0 | 2 | 2 |
ATAC-seq | 5 | 8 | 10 | |
Pol II ChIP-seq | 0 | 0 | 0 | |
Lower 10% + winsorization | H3K27ac ChIP-seq | 237 | 789 | 1442 |
ATAC-seq | 1050 | 2171 | 3197 | |
Pol II ChIP-seq | 303 | 990 | 1546 | |