nameUpdator: Used to update marker names

In MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

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)

MetaCyto documentation built on Nov. 8, 2020, 7:50 p.m.