fcsInfoParser {MetaCyto} | R Documentation

## Organize fcs files in a study from ImmPort into panels

### Description

A function that organizes fcs files in a study from ImmPort into panels.

### Usage

    fcsInfoParser(metaData, studyFolder, fcsCol = "ZBXFN", assay = c("FCM",
      "CyTOF"))

### Arguments

`metaData` | A data frame. Must contain a column listing the names of fcs files included in the study.
`studyFolder` | Path of the directory containing all the files of a study from ImmPort.
`fcsCol` | A string specifying the name of the column in metaData that lists fcs files included in the study.
`assay` | Either "FCM" or "CyTOF" to indicate the type of cytometry data.

### Value

A dataframe containing 2 columns: a column called "fcs_files" that contains the location (relative to the working directory) of each fcs file on the hard drive and a column called "study_id" that specify what study each fcs file belongs to.

### Examples

    fn=system.file("extdata",
                  "SDY736/SDY736-DR19_Subject_2_Flow_cytometry_result.txt",
                  package="MetaCyto")
    meta_data=read.table(fn,sep='\t',header=TRUE, check.names= FALSE)
    # Organize fcs file into panels
    fn=system.file("extdata","SDY736",package="MetaCyto")
    fcs_info_SDY736=fcsInfoParser(metaData=meta_data,
                                  studyFolder=fn,
                                  fcsCol="File Name",
                                  assay="FCM")

[Package MetaCyto version 1.2.1 Index]