cytof_writeResults: Save the cytofkit analysis results

In haoeric/cytofkit_devel: cytofkit: an integrated mass cytometry data analysis pipeline

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

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 save the results object into RData file, for loading back to R and to shiny APP.
saveToFCS	boolean value determines if save the results back to the FCS files, new FCS files will be generated under folder XXX_analyzedFCS.
saveToFiles	boolean value determines if parse the results and automatically save 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	boolean if inverse logicle transform the cluster cor1 and cor2 channels.

Value

save all results in the resultDir

See Also

cytofkit

Examples

d <- system.file('extdata',package='cytofkit')
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)

haoeric/cytofkit_devel documentation built on May 17, 2019, 2:29 p.m.