nameUpdator {MetaCyto} | R Documentation

## Used to update marker names

### Description

A function that updates marker names in the files output by the preprocessing.batch function.

### Usage

    nameUpdator(oldNames, newNames, files)

### Arguments

`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.

### Value

Null

### Examples

    #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)

[Package MetaCyto version 1.12.0 Index]