Compute the transcription start site (TSS) enrichment score for each cell, as defined by ENCODE: https://www.encodeproject.org/data-standards/terms/.
TSSEnrichment( object, tss.positions = NULL, n = NULL, fast = TRUE, assay = NULL, cells = NULL, process_n = 2000, verbose = TRUE, region_extension = 1000 )
A Seurat object
A GRanges object containing the TSS positions. If NULL, use the genomic annotations stored in the assay.
Number of TSS positions to use. This will select the first _n_ TSSs from the set. If NULL, use all TSSs (slower).
Just compute the TSS enrichment score, without storing the base-resolution matrix of integration counts at each site. This reduces the memory required to store the object but does not allow plotting the accessibility profile at the TSS.
Name of assay to use
A vector of cells to include. If NULL (default), use all cells in the object
Number of regions to process at a time if using
Distance extended upstream and downstream from TSS in which to calculate enrichment and background.
The computed score will be added to the object metadata as "TSS.enrichment".