I want to find the master transcription factors (the transcription factors that govern the highest number of genes) per cell type in my animal. I will have single cell ATAC-seq and single cell RNAseq data. I was thinking of using the RNAseq data to group cells into metacells, then finding the most highly accessible peaks in those metacells using Chromvar. Would I be using as input the consensus peak set per metacell and then use the consensus peak set from all cells from all metacells as background? I am still a little confused about how Chromvar works after reading the Nature Methods paper and the online vignette.