SelectGenePeaks: Return peaks associated with a select gene.

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

Return peaks associated with a select gene.

Description

Returns peaks associated with a select gene.

Usage

SelectGenePeaks(
  peaks.object,
  gene,
  feature.type = c("UTR3", "UTR5", "exon", "intron")
)

Arguments

peaks.object	Peaks SCE or Seurat object.
gene	Gene name
feature.type	type of genomic features to use

Value

a list of peak IDs

Examples

extdata_path <- system.file("extdata",package = "Sierra")
load(paste0(extdata_path, "/Cxcl12_example.RData"))
load(paste0(extdata_path, "/TIP_cell_info.RData"))

## Create an suerat object holding the peak data
peaks.seurat <- NewPeakSeurat(peak.data = peak.counts, 
                        annot.info = peak.annotations, 
                        cell.idents = tip.populations, 
                        tsne.coords = tip.tsne.coordinates,
                        min.cells = 0, min.peaks = 0)

peak.list <- SelectGenePeaks(peaks.object =  peaks.seurat ,gene = "Cxcl12")

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