Supplementary Figure 2: Background peak set selection.
From: chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
(a) Raw accessibility deviations for GM12878 cells for peak sets based on GC content. Peaks were grouped into 10 bins based lowest to highest GC content. Two cells are highlighted in orange and purple. (b) Same as (a) except bins defined by average accessibility across the cells. (c) GC content versus average accessibility for a sample of peaks. (d) Same data from (c) after Mahalanobis transformation. Peaks are placed into “bins” based on the values of this transformed data; the grid lines show example bins. e) For the peak indicated with the yellow diamond, the probability of selecting a peak from within a given bin as its background peak. f) Similar to (e), but showing the probability of selecting an individual peak as the background peak for the indicated peak in terms of the untransformed space. (g-i) Distribution of GC content per peak for all peaks (grey), the given motif of interest (black), and a background set for that motif (red). (j-l) Distribution of average fragment count per peak (log10) for all peaks (grey), the given motif of interest (black), and a background set for that motif (red).
