getQuantiles: getQuantiles

In saeyslab/CytoNorm: Normalisation of cytometry data measured across multiple batches

getQuantiles

Description

getQuantiles

Usage

getQuantiles(
  files,
  channels,
  nQ = 99,
  minCells = 50,
  quantileValues = NULL,
  transformList = NULL,
  labels = NULL,
  selection = NULL,
  verbose = FALSE,
  plot = FALSE,
  ...
)

Arguments

files	Full paths of to the fcs files of the samples
channels	Names of the channels to compute the quantiles for
nQ	Number of quantiles to compute Default = 99, which results in quantiles for every percent of the data. Ignored if quantileValues is given.
minCells	Minimum number of cells required to compute trust-worthy quantiles. Otherwise NA is returned. Default = 50.
quantileValues	Vector of length with values between 0 and 1, giving the percentages at which the quantiles should be computed. If NULL (default), the quantiles will be evenly distributed, including 0 and 1.
transformList	Transformation list to pass to the flowCore transform function
labels	A label for every file, indicating to which group it belongs. If multiple files have the same label, they get aggregated. If NULL, all files are handled separately.
selection	List with indexation vector for every file.
verbose	If TRUE, extra output is printed. Default = FALSE
plot	If TRUE, plots are generated showing all quantiles. Default = FALSE.
...	Additional arguments to pass to read.FCS

Examples

dir <- system.file("extdata", package = "CytoNorm")
files <- list.files(dir, pattern = "fcs$")

ff <- flowCore::read.FCS(file.path(dir, files[1]))
channels <- grep("Di$", flowCore::colnames(ff), value = TRUE)
transformList <- flowCore::transformList(channels,
                                         cytofTransform)

quantiles <- getQuantiles(files = file.path(dir, files),
                          channels = channels,
                          transformList = transformList)

pheatmap::pheatmap(quantiles[[1]],
                   cluster_rows = FALSE,
                   cluster_cols = FALSE,
                   labels_col =
                     paste0(FlowSOM::GetMarkers(ff, colnames(quantiles[[1]])),
                            " (", colnames(quantiles[[1]]), ")"),
                   main = files[1])

saeyslab/CytoNorm documentation built on Nov. 2, 2024, 12:39 p.m.