sampleInfoParser {MetaCyto} | R Documentation

## Collect sample information for fcs files in a study from ImmPort.

### Description

A function that collects sample information for fcs files in a study from ImmPort.

### Usage

    sampleInfoParser(metaData, studyFolder, fcsCol = "ZBXFN", assay = "FCM",
      attrCol)

### 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.
`attrCol` | A vector of column names. Used to specify the information about each cytometry the user wish to include in the analysis.

### Value

A dataframe containing sample information.

### 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)
    # Find the AGE, GENDER info from selected_data
    fn=system.file("extdata","SDY736",package="MetaCyto")
    sample_info_SDY736=sampleInfoParser(metaData=meta_data,
                                        studyFolder=fn,
                                        assay="FCM",
                                        fcsCol="File Name",
                                        attrCol=c("Subject Age","Gender"))

[Package MetaCyto version 1.2.1 Index]