CountPeaks: Generate a peak x cell UMI count matrix

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

Generate a peak x cell UMI count matrix

Description

Generates a UMI count matrix where rows are the peaks and columns are the cells. Counts cells that are identified through a provided 'white list' of cell barcodes. If alignment done using CellRanger, this will be the barcodes.tsv file contained in the 'filtered_gene_matrices_mex' folder for example.

Usage

CountPeaks(
  peak.sites.file,
  gtf.file,
  bamfile,
  whitelist.file,
  output.dir,
  countUMI = TRUE,
  ncores = 1,
  chr.names = NULL,
  filter.chr = FALSE,
  gene.symbol.ref = "gene_name",
  CBtag = "CB",
  UMItag = "UB"
)

Arguments

peak.sites.file	a file containing peak coordinates generated by FindPeaks
gtf.file	reference (GTF) file
bamfile	scRNA-seq BAM file
whitelist.file	file of cell barcodes to count
output.dir	name of directory to write output (will be created if it doesn't exist)
countUMI	whether to count UMIs (default: TRUE)
ncores	Number of cores for multithreading
chr.names	names of chromosomes
filter.chr	names of chromosomes to filter
gene.symbol.ref	field in the GTF file containing the gene symbol
CBtag	cell barcode tag identifier present in BAM file. Default 'CB'.
UMItag	UMI barcode tag identifier present in BAM file. Default 'UB'.

Value

NULL. Writes counts to file.

Examples

extdata_path <- system.file("extdata",package = "Sierra")
reference.file <- paste0(extdata_path,"/Vignette_cellranger_genes_subset.gtf")

bamfile <- c(paste0(extdata_path,"/Vignette_example_TIP_sham.bam"),
             paste0(extdata_path,"/Vignette_example_TIP_mi.bam") )
             
whitelist.bc.file <- paste0(extdata_path,"/example_TIP_sham_whitelist_barcodes.tsv")
  
peak.merge.output.file = paste0(extdata_path, "/TIP_merged_peaks.txt")
 
## Not run:                                 
CountPeaks(peak.sites.file = peak.merge.output.file, 
             gtf.file = reference.file,
             bamfile = bamfile[1], 
             whitelist.file = whitelist.bc.file[1],
             output.dir = count.dirs[1], 
             countUMI = TRUE, 
             ncores = 1)
 
## End(Not run)

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