scTssQC: Compute TSS enrichment score per cell

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

Compute TSS enrichment score per cell

Description

Compute TSS enrichment score per cell

Usage

scTssQC(
  object = NULL,
  gene.annotation = NULL,
  n = NULL,
  cells = NULL,
  process_n = 2000,
  verbose = TRUE
)

Arguments

object	A Fragment object, must contain slot 'cells'.
gene.annotation	A GRanges object containing the TSS positions.
n	Number of TSS positions to use. This will select the first _n_ TSSs from the set. If NULL, use all TSSs (slower).
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 fast option.
verbose	Display messages

Details

Compute the transcription start site (TSS) enrichment score for each cell, as defined by ENCODE: https://www.encodeproject.org/data-standards/terms/.

Value

Returns two matrix

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.