sampleInfoParser: Collect sample information for fcs files in a study from...
In MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

Description Usage Arguments Value Examples

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

1 2	sampleInfoParser(metaData, studyFolder, fcsCol = "ZBXFN", assay = "FCM", attrCol)

`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.

A dataframe containing sample information.

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"))