GetExpressedPeaks: Identify peaks expressed within a certain percentage of cells

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

Identify peaks expressed within a certain percentage of cells

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

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

Arguments

peaks.object	the peaks object either Seurat of SingleCellExperiment class.
population.1	target cluster
population.2	background cluster. If NULL (deafult) all non-target 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_highly_expressed_peaks(seurat.object, "1")
    get_highly_expressed_peaks(seurat.object, cluster1 = "1", cluster2 = "2")
 
## End(Not run)

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