fcsInfoParser {MetaCyto} | R Documentation |
A function that organizes fcs files in a study from ImmPort into panels.
fcsInfoParser(metaData, studyFolder, fcsCol = "ZBXFN", assay = c("FCM", "CyTOF"))
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. |
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.
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")