ProcessMultipleFiles {Sconify} | R Documentation |
This is tailored to a very specific file format for unstim/stim Files need the following name convention: "xxxx_stim.fcs" Files where you want to name the patients need the following convention: "xxxx__patientID_stim.fcs"
ProcessMultipleFiles(files, transform = "asinh", numcells = 10000, norm = FALSE, scale = FALSE, input, name.multiple.donors = FALSE)
files |
a vector of file names (name = "anything_condition.fcs") |
transform |
set to asinh if you want to do an asinh transform of all markers in the dataset |
numcells |
desiered number of cells in the matrix, set at 10k |
norm |
boolean that quantile normalizes the data if true |
scale |
boolean that converts all values to z scores if true |
input |
the static markers that will be used downstream in knn computation. These are included here to include the option of per-marker quantile normalization, in the event norm is set to TRUE |
name.multiple.donors |
boolean indicating whether multiple donors will be distinguished (as a separate "patient" column) |
result: a combined file set
file1 <- system.file("extdata", "Bendall_et_al_Cell_Sample_C_basal.fcs", package = "Sconify") file2 <- system.file("extdata", "Bendall_et_al_Cell_Sample_C_IL7.fcs", package = "Sconify") ProcessMultipleFiles(c(file1, file2), input = input.markers)