Figure 3.
Differential accessibility analysis with PeakVI
(A) Illustration of the different comparisons. “real,” compare cells between two population; “null,” compare cells from different batches within a single population; “real b1”/“real b2,” compare cells from a specific batch in a population to all cells in the other population.
(B) Pearson correlations between the estimated and empirical effects.
(C) Correlation of effect size in “real b1” and corresponding effect in “real b2” comparisons. PeakVI estimated effects are far less sensitive to batch effects.
(D) An example (using cluster 14) relationship between the PeakVI estimated effect to the empirical effect in real (top) and null (bottom) comparisons.
(E) The width (measured by the SD) of the effect distributions; PeakVI amplifies real differential effects, and silences nuisance ones.
(F) Level of amplification/silencing depends on level of noise in the empirical effect.
(G) Volcano plots for a GLM (top), Wilcoxon (middle), and PeakVI (bottom) when comparing between two batches of NK cells.
(H) Volcano plots for a GLM (top), Wilcoxon (middle), and PeakVI (bottom) when comparing between B cells and NK cells.
(I) PeakVI (bottom) effect is better correlated with a bulk ATAC-based ground truth comparison and more numerically stable than GLM (top) and Wilcoxon (middle).