fcs2DF {CytoDx} | R Documentation |
A function that convert fcs files to a data frame.
fcs2DF(fcsFiles, y = NULL, assay = c("FCM", "CyTOF"), b = 1/200, fileSampleSize = 5000, compFiles = NULL, nameDict = NULL, excludeTransformParameters = c("FSC-A", "FSC-W", "FSC-H", "Time", "Cell_length"))
fcsFiles |
A vector specifying the location of fcs files (relative to working directory). |
y |
A vector containing the clinical outcome of each sample. Must have the same length as fcsFiles. Null for testing data. |
assay |
Either "FCM" or "CyTOF" to indicate the type of cytometry data. |
b |
A positive number used to specify the arcsinh transformation. f(x) = asinh (b*x) where x is the original value and f(x) is the value after transformation. The suggested value is 1/150 for flow cytometry (FCM) data and 1/8 for CyTOF data. |
fileSampleSize |
An integer specifying the number of events sampled from each fcs file. If NULL, all the events will be pre-processed and wrote out to the new fcs files. |
compFiles |
A vector specifying the paths of user supplied compensation matrix for each fcs file. The matrix must be stored in csv files. |
nameDict |
A vector used to change marker names.Each element in the vector is the prefered name of a marker. The name of each element is the marker name used in the fcs file. For example, a vector c("CD8b"="CD8","cd8"="CD8") will change "CD8b" and "cd8" into "CD8", making annotations more consistent. |
excludeTransformParameters |
A vector specifying the name of parameters not to be transformed (left at linear scale). |
Returns a data frame containing the preprocessed cytometry data. Cells from different fcs files are combined into one flow frame. A new column, xSample, is introduced to indicate the origin of each cell. The data frame also includes the clinical outcome y.
# Find the table containing fcs file names in CytoDx package path <- system.file("extdata",package="CytoDx") # read the table fcs_info <- read.csv(file.path(path,"fcs_info.csv")) # Specify the path to the cytometry files fn <- file.path(path,fcs_info$fcsName) # Read cytometry files using fcs2DF function train_data <- fcs2DF(fcsFiles=fn, y=fcs_info$Label, assay="FCM", b=1/150, excludeTransformParameters= c("FSC-A","FSC-W","FSC-H","Time"))