get_expressed_peaks_sce: Identify highly expressed peaks

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Identify highly expressed peaks

Description

Selects peaks that are considered expressed above some provided criteria within a target or background cluster. Considers peaks expressed in some x% of cells to be highly expressed. Returns the union of peaks identified from the target and background cluster

Usage

get_expressed_peaks_sce(
  peaks.sce.object,
  population.1,
  population.2 = NULL,
  threshold = 0.05
)

Arguments

peaks.sce.object	the peak-count SCE object
population.1	target population
population.2	background population If NULL (deafult) all non-population.1 cells
threshold	percentage threshold of detected (non-zero) expression for including a peak

Value

an array of peak (or gene) names

Examples

## Not run: 
get_expressed_peaks_sce(peak.sce, "1")
get_expressed_peaks_sce(peak.sce, population.1 = "1", population.2 = "2")

## End(Not run)

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.