gate_singlet_cells: Gate singlet cells

In prybakowska/CytoQP: Cytometry data quality control and cleaninig

Gate singlet cells

Description

Detects outliers in the selected channel(s) using MAD (mean absolute deviation).

Usage

gate_singlet_cells(
  flow_frame,
  file_name = NULL,
  channels = "Event_length",
  arcsine_transform = TRUE,
  save_gated_flow_frame = NULL,
  suffix = "_singlets_gated",
  n_mad = 2,
  out_dir = NULL,
  ...
)

Arguments

flow_frame	A flowframe that contains cytometry data.
file_name	Character, the file name used for saving the flow frame (if save_gated_flow_frame = TRUE) and for plotting, if NULL (default) the file name stored in keyword FIL will be used.
channels	character, channels name to be used for gating, default is to Event_length.
arcsine_transform	Logical, if the data should be transformed with arcsine transformation and cofactor 5. If FALSE the data won't be transformed, thus transformed flow frame should be used if needed. Default TRUE.
save_gated_flow_frame	Logical, if gated flow frame should be saved. Only cells falling into intact cell region will be saved. Default set to FALSE.
suffix	Character, suffix placed in the name of saved fcs file, only if save_gated_flow_frame = TRUE. Default is "_singlets_gated".
n_mad	Numeric, number of MADs to detect outliers.Default set to 2.
out_dir	Character, pathway to where the files should be saved, if NULL (default) files will be saved to file.path(getwd(), Gated).
...	Additional arguments to pass to flowDensity::plotDens().

Value

An untransformed flow frame with singlets only

Examples

#' # Set input directory
aggregate_dir <- file.path(dir, "Aggregated")

# List files for gating
files <- list.files(path = aggregate_dir,
                    pattern = ".fcs$",
                    full.names = TRUE)

# Create directory to store plot
gate_dir <- file.path(getwd(), "Gated")
if(!dir.exists(gate_dir)){dir.create(gate_dir)}

# Gate the files and plot the gating strategy for each file
n_plots <- 1
png(file.path(gate_dir, paste0("gating.png")),
    width = n_plots * 300, height = length(files) * 300)
layout(matrix(1:(length(files) * n_plots), ncol = n_plots, byrow = TRUE))

for (file in files){

 ff <- flowCore::read.FCS(filename = file,
                          transformation = FALSE)

 ff <- gate_singlet_cells(flow_frame = ff,
                          channels = "Event_length",
                         file_name = basename(file), save_gated_flow_frame = TRUE)
}

dev.off()

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