fcsInfoParser: Organize fcs files in a study from ImmPort into panels

In hzc363/MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

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")

hzc363/MetaCyto documentation built on July 27, 2020, 2:46 a.m.