sampleInfoParser {MetaCyto} | R Documentation |
A function that collects sample information for fcs files in a study from ImmPort.
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"))