nameUpdator {MetaCyto} | R Documentation |
A function that updates marker names in the files output by the preprocessing.batch function.
nameUpdator(oldNames, newNames, files)
oldNames |
A vector of marker names you wish to change |
newNames |
A vector of marker names you wish each oldNames to be changed to. |
files |
A list of "processed_sample_summary.csv" files output by the preprocessing.batch function, in which the name change will occur. |
Null
#get meta-data fn=system.file("extdata","fcs_info.csv",package="MetaCyto") fcs_info=read.csv(fn,stringsAsFactors=FALSE,check.names=FALSE) fcs_info$fcs_files=system.file("extdata",fcs_info$fcs_files, package="MetaCyto") # make sure the transformation parameter "b" and the "assay" argument # are correct of FCM and CyTOF files b=assay=rep(NA,nrow(fcs_info)) b[grepl("CyTOF",fcs_info$study_id)]=1/8 b[grepl("FCM",fcs_info$study_id)]=1/150 assay[grepl("CyTOF",fcs_info$study_id)]="CyTOF" assay[grepl("FCM",fcs_info$study_id)]="FCM" # preprocessing preprocessing.batch(inputMeta=fcs_info, assay=assay, b=b, outpath="Example_Result/preprocess_output", excludeTransformParameters=c("FSC-A","FSC-W","FSC-H", "Time","Cell_length")) # Make sure marker names are consistant in different studies files=list.files("Example_Result",pattern="processed_sample",recursive=TRUE, full.names=TRUE) nameUpdator("CD8B","CD8",files)