LoadMultiCleanFCS: LoadMultiCleanFCS

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

LoadMultiCleanFCS

Description

LoadMultiCleanFCS returns a list of FCS file data, where each member is a list that contains dataframe from different conditions from different timepoints.

Usage

LoadMultiCleanFCS(
  list.of.file.names,
  channel.remove,
  channel.annotate,
  subsamples = 1000,
  transform = TRUE
)

Arguments

list.of.file.names	A list where each member contains 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 list containing multiple dataframes containing single-cell data from the same timepoint, but multiple conditions

Examples

list.of.file.names <- list("1" = c("Desktop/A-1.fcs", "Desktop/B-1.fcs"),
"2" = c("Desktop/A-2.fcs", "Desktop/B-2.fcs"))
var.remove <- c("Channel3", "Channel4")
var.annotate <- list("c1" = "Channel1", "c2" = "Channel2",
"c3" = "Channel3", "c4" = "Channel4")

LoadMultiCleanFCS(list.of.file.names, var.remove, var.annotate, subsamples = 100, transform = TRUE)

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