scTssQC: Compute TSS enrichment score per cell

scTssQCR Documentation

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/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.