cytof_writeResults: Save the cytofkit analysis results

In JinmiaoChenLab/cytofkit2: cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

Save the cytofkit analysis results

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 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

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)

JinmiaoChenLab/cytofkit2 documentation built on May 12, 2022, 8:09 a.m.