cytof_writeResults: Save the cytofkit analysis results

Description Usage Arguments Value See Also Examples

View source: R/cytof_postProcess.R

Description

Save analysis results from cytofkit main function to RData, csv files and PDF files and add them to a new copy of FCS files.

Usage

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cytof_writeResults(analysis_results, projectName, saveToRData = TRUE,
  saveToFCS = TRUE, saveToFiles = TRUE, resultDir, rawFCSdir,
  inverseLgclTrans = TRUE)

Arguments

analysis_results

Result data from output of cytofkit

projectName

A prefix that will be added to the names of result files.

saveToRData

Boolean value determines if results object is saved into RData file, for loading back to R and to shiny APP.

saveToFCS

Boolean value determines if results are saved back to FCS files, new FCS files will be generated under folder XXX_analyzedFCS.

saveToFiles

Boolean value determines if results are parsed and automatically saved to csv files and pdf figures.

resultDir

The directory where result files will be generated.

rawFCSdir

The directory that contains fcs files to be analysed.

inverseLgclTrans

If TRUE, inverse logicle transform the cluster cor1 and cor2 channels.

Value

Save all results in the resultDir

See Also

cytofkit

Examples

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d <- system.file('extdata',package='cytofkit2')
f <- list.files(d, pattern='.fcs$', full=TRUE)
p <- list.files(d, pattern='.txt$', full=TRUE)
#tr <- cytofkit(fcsFile=f,markers=p,projectName='t',saveResults=FALSE)
#cytof_write_results(tr,projectName = 'test',resultDir=d,rawFCSdir =d)

raman91/cytofkit2 documentation built on Dec. 22, 2021, 12:54 p.m.