Compute TSS enrichment score per cell — TSSEnrichment • Signac

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,
  assay = NULL,
  cells = NULL,
  verbose = TRUE
)

Arguments

object	A Seurat object
tss.positions	A GRanges object containing the TSS positions
assay	Name of assay to use
cells	A vector of cells to include. If NULL (default), use all cells in the object
verbose	Display messages

Value

Returns a Seurat object

Details

The computed score will be added to the object metadata as "TSS.enrichment".

Examples

if (FALSE) {
library(EnsDb.Hsapiens.v75)
gene.ranges <- genes(EnsDb.Hsapiens.v75)
gene.ranges <- gene.ranges[gene.ranges$gene_biotype == 'protein_coding', ]
tss.ranges <- GRanges(
  seqnames = seqnames(gene.ranges),
  ranges = IRanges(start = start(gene.ranges), width = 2),
  strand = strand(gene.ranges)
)
seqlevelsStyle(tss.ranges) <- 'UCSC'
tss.ranges <- keepStandardChromosomes(tss.ranges, pruning.mode = 'coarse')

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
atac_small <- SetFragments(object = atac_small, file = fpath)
TSSEnrichment(object = atac_small, tss.positions = tss.ranges[1:100])
}