ProcessMultipleFiles {Sconify} | R Documentation

## Converts multiple files into a concatenated data frame

### 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)

[Package Sconify version 1.2.1 Index]