process_ltbc: Process Lineage Tracing Barcodes

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Process Lineage Tracing Barcodes

Description

Process Lineage Tracing Barcodes

Usage

process_ltbc(
  sobject,
  cid_lt,
  histogram = FALSE,
  col_fill = "#4DBBD5FF",
  ymax = NA,
  relative = FALSE,
  title = "LT Barcode Frequency",
  ret_list = FALSE
)

Arguments

sobject	Name of the Seurat object that contains the cell barcodes (cids) that will be matched and integrated
cid_lt	Table of cellecta cell id and lineage tracing barcodes. Returned by gen_cellecta_bc_data()
histogram	Will trigger the function to generate and output a histogram plot of the top 40 most frequent lineage tracing barcodes
col_fill	Fill color
ymax	Upper limit of the y axis (ie, for creating side-by-side comparisons)
relative	This will normalize cell counts to total number of cells containing barcodes
title	Title of the histogram, if generated
ret_list	If TRUE, return a list of barcode frequencies instead of a Seurat object

Value

either a Seurat object or a data frame of barcode frequences

Examples

## Not run: 
cid_lt <- gen_cellecta_bc_data(file = "path/to/file.bam",
                               verbose = TRUE,
                               samtools_module = "GCC/9.3.0 SAMtools/1.10")
output <- process_ltbc(sobject, cid_lt = cid_lt, histogram = TRUE)

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.