Supplementary Figure 5: Effects of varying number of background iterations, sequence bias correction, and peak width.
From: chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
(a) RMSD and normalized RMSD of variability when using a given number of background sets relative to when using 1000 background sets. Normalized RMSD is RMSD divided by the range of the variability when using 1000 background sets. (b) Same as (a) but for normalized deviations instead of variability. (c) Same as (a) but for deviation Z-scores instead of variability. (d) Correlation between Tn5 bias model average versus GC content for peaks used in scATAC-seq analysis, (e) Correlation in bias-corrected deviations per motif using GC content versus Tn5 bias model for background peak selection versus variability (determined using GC content for bias). (f) Variability of motifs across cells using either Tn5 bias model or GC content for background peak selection. (g-h) chromVAR was run using peaks fixed to a width of 100bp, 250bp, 500bp, 750bp, or 1000bp based on windows around MACS2 summits or using the peaks output directly from MACS2 (variable width). (g) Correlation of the bias corrected deviations for the top 50 most variable TF motifs when using different peak width choices. (h) Correlation of the variability for different motifs when using different peak width choices. (i) Average variability for the top 50 most variable motifs when using different peak width choices. For determining the top 50 most variable motifs in (h) and (i), the top 50 from each peak width strategy were included.
