searchCluster.batch {MetaCyto}

R Documentation

Search for clusters using pre-defined labels in cytometry data from different studies in batch

Description

A function that searches for clusters using pre-defined labels in cytometry data from different studies in batch.

Usage

searchCluster.batch(preprocessOutputFolder, outpath = "search_output",
  clusterLabel, ifPlot = TRUE)

Arguments

preprocessOutputFolder	Directory where the pre-processed results are stored.
outpath	A string indicating the directory the results should be written to.
clusterLabel	A vector containing labels, such as c("CD3+|CD4+|CD8-")
ifPlot	True or False. Used to specify if a the density plot for each cluster should be plotted

Details

The function writes out the summary statistics for each cluster. A separate directory will be created for each study.

Value

Results will be written to the outpath folder

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)
# find the clusters
cluster_label=c("CD3-|CD19+","CD3+|CD4-|CD8+")
searchCluster.batch(preprocessOutputFolder="Example_Result/preprocess_output",
                    outpath="Example_Result/search_output",
                    clusterLabel=cluster_label)

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