LoadCleanFCS: LoadCleanFCS

In zunderlab/FLOWMAP: Graph-based visualizations of high-dimensional single-cell data across time

LoadCleanFCS

Description

LoadCleanFCS returns a list of FCS file data, where each member is a dataframe from a different timepoint. In the mode "single", the list has only a single element, a dataframe from the one FCS file path provided.

Usage

LoadCleanFCS(
  fcs.file.names,
  channel.remove,
  channel.annotate,
  subsamples = 1000,
  transform = TRUE
)

Arguments

fcs.file.names	A vector of full file paths to the FCS files to be used
channel.remove	Vector naming channels to be removed from all loaded FCS data
channel.annotate	List mapping channel names to user-specified names to properly annotate all FCS file data
subsamples	Numeric or vector of numerics specifying how many cells to sample from each FCS file, default is set to 1000
transform	Logical specifying whether to transform the data using an Asinh transform typical of CyTOF/mass cytometry datasets, default is set to TRUE

Value

a list where each member is a dataframe containing the single-cell data

Examples

fcs.file.names <- c("Desktop/A.fcs", "Desktop/B.fcs")
var.remove <- c("Channel3", "Channel4")
var.annotate <- list("c1" = "Channel1", "c2" = "Channel2",
"c3" = "Channel3", "c4" = "Channel4")

LoadCleanFCS(fcs.file.names, var.remove, var.annotate, subsamples = 100, transform = TRUE)

zunderlab/FLOWMAP documentation built on Sept. 7, 2024, 6:31 p.m.