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 )
object | A Seurat object |
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tss.positions | A GRanges object containing the TSS positions. If NULL, use the genomic annotations stored in the assay. |
n | Number of TSS positions to use. This will select the first _n_ TSSs from the set. If NULL, use all TSSs (slower). |
fast | 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. |
assay | Name of assay to use |
cells | A vector of cells to include. If NULL (default), use all cells in the object |
process_n | Number of regions to process at a time if using |
verbose | Display messages |
Returns a Seurat
object
The computed score will be added to the object metadata as "TSS.enrichment".
if (FALSE) { fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac") Fragments(atac_small) <- CreateFragmentObject( path = fpath, cells = colnames(atac_small), tolerance = 0.5 ) TSSEnrichment(object = atac_small) }