cytof_writeResults: Save the cytofkit analysis results
In raman91/cytofkit2: cytofkit: an integrated mass cytometry data analysis pipeline

Description Usage Arguments Value See Also Examples

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

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

`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.

Save all results in the resultDir

cytofkit

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)