debarcode_files: Debarcodes files

In prybakowska/CytoQP: Cytometry data quality control and cleaninig

Debarcodes files

Description

Performs sample debarcoding.

Usage

debarcode_files(
  fcs_files,
  cores = 1,
  file_batch_id,
  file_score = NULL,
  out_dir = NULL,
  min_threshold = TRUE,
  threshold = 0.18,
  to_plot = TRUE,
  barcodes_used = NULL,
  less_than_th = FALSE,
  barcode_key = NULL
)

Arguments

fcs_files	Character, full path to fcs_files.
cores	Number of cores to be used
file_batch_id	Character vector with batch label for each fcs_file, the order and the length needs to be the same as in fcs_files. If only batch is processed can be prepared as e.g. file_batch_id <- rep("batch", length(files))
file_score	Data frame with quality scores obtained from file_quality_check.Default set to NULL.
out_dir	Character, pathway to where the plots should be saved, only if argument to_plot = TRUE, default is set to working directory
min_threshold	Logical, if the minimal threshold for barcoding should be applied.Default set to TRUE.
threshold	Numeric, value for the minimum threshold for debarcoding, default is set to 0.18, only if min_threshold set to TRUE.
to_plot	Logical, if plots for yields and debarcoding quality should be plotted.
barcodes_used	Character vector with the names of the barcodes that were used, eg. barcode 1 is the same as A1. Or a list with the barcodes name per batch. If NULL (default) all the barcodes contained in sample_key will be used, regarding the batch.
less_than_th	Logical, if the name of the files for which lower threshold than set in parameter threshold was detected. Default is set to FALSE.
barcode_key	matrix as in CATALYST::assignPrelim, the debarcoding scheme. A binary matrix with sample names as row names and numeric masses as column names OR a vector of numeric masses corresponding to barcode channels. When the latter is supplied, 'assignPrelim' will create a scheme of the appropriate format internally.

Value

Save debarcoded fcs files in out_dir. If parameter to_plot set to TRUE, save plots for yields and debarcodig quality in out_dir. If less_than_th set to TRUE, save file names for which threshold lower than in parameter threshold was detected "files_with_lower_debarcoding_threshold.RDS" in out_dir.

Examples

# Set input directory
clean_dir <- file.path(dir, "Cleaned")

# Define files for debarcoding
files <- list.files(clean_dir,
                   pattern = "_cleaned.fcs$",
                   full.names = TRUE)

# Read in file scores if calculated
file_scores <- readRDS(list.files(path = dir,
                                 recursive = TRUE,
                                 full.names = TRUE,
                                 pattern = "Quality_AOF_score.RDS"))

# Define file batch ID for each file
file_batch_id <- stringr::str_match(basename(files),
                                   "(day[0-9]*).*.fcs")[,2]

# Read in metadata
md <- utils::read.csv(file.path(dir, "RawFiles", "meta_data.csv"))

# read in barcode key
sample_key <- CATALYST::sample_key
# Extract information about barcodes used in each batch
barcodes_list <- list()
for (batch in unique(file_batch_id)){
 idx <- md[md[,"BATCH"] == batch, "BARCODE"]
 barcodes_list[[batch]] <- rownames(sample_key)[idx]
}

# Debarcode files
debarcode_files(fcs_files = files,
               out_dir = NULL,
               file_score = file_scores,
               min_threshold = TRUE,
               barcodes_used = barcodes_list,
               file_batch_id = file_batch_id,
               less_than_th = TRUE,
               barcode_key = sample_key)

prybakowska/CytoQP documentation built on June 28, 2022, 12:36 a.m.