View source: R/load-from-FCS.R
LoadMultiCleanFCS | R Documentation |
LoadMultiCleanFCS
returns a list of FCS file data, where each member is
a list that contains dataframe from different conditions from different timepoints.
LoadMultiCleanFCS(
list.of.file.names,
channel.remove,
channel.annotate,
subsamples = 1000,
transform = TRUE
)
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 |
transform |
Logical specifying whether to transform the data using an Asinh
transform typical of CyTOF/mass cytometry datasets, default is set to |
a list where each member is a list containing multiple dataframes containing single-cell data from the same timepoint, but multiple conditions
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)
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