ProcessMultipleFiles: Converts multiple files into a concatenated data frame

In Sconify: A toolkit for performing KNN-based statistics for flow and mass cytometry data

Description

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"

Usage

ProcessMultipleFiles(files, transform = "asinh", numcells = 10000,
  norm = FALSE, scale = FALSE, input, name.multiple.donors = FALSE)

Arguments

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)

Value

result: a combined file set

Examples

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)

Sconify documentation built on Nov. 8, 2020, 6:45 p.m.