champ.process: Process function to run all methods in ChAMP pipeline.

In JoshuaTian/MyChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Description

This function allows the user to run the entire pipeline in one function. Arguments allow user to select functions if desired. Note that it maybe run during champ.process() if there is any problem during the process, thus run ChAMP functions one by one is actually recommended.

Usage

    champ.process(runload=TRUE,
                  directory = getwd(),
                  filters=c("XY","DetP","Beads","NoCG","SNP","MultiHit"),
                  #---champ.impute parameters below---#
                  runimpute=TRUE,
                  imputemethod="Combine",
                  #---champ.QC parameters below---#
                  runQC=TRUE,
                  QCplots=c("mdsPlot","densityPlot","dendrogram"),
                  #---champ.norm parameters below---#
                  runnorm=TRUE,
                  normalizationmethod="BMIQ",
                  #---champ.SVD parameters below---#
                  runSVD=TRUE,
                  RGEffect=FALSE,
                  #---champ.runCombat parameters below---#
                  runCombat=TRUE,
                  batchname=c("Slide"),
                  #---champ.DMP parameters below---#
                  runDMP=TRUE,
                  #---champ.DMR parameters below---#
                  runDMR=TRUE,
                  DMRmethod="Bumphunter",
                  #---champ.Block parameters below---#
                  runBlock=TRUE,
                  #---champ.GSEA parameters below---#
                  runGSEA=TRUE,
                  #---champ.EpiMod parameters below---#
                  runEpiMod=TRUE,
                  #---champ.CNA parameters below---#
                  runCNA=TRUE,
                  control=TRUE,
                  controlGroup="champCtls",
                  #---champ.reffree parameters below---#
                  runRefFree=TRUE,
                  #---champ.refbase parameters below---#
                  runRefBase=FALSE,
                  #---universal settings---#
                  compare.group=NULL,
                  adjPVal=0.05,
                  resultsDir="./CHAMP_RESULT/",
                  arraytype="450K",
                  PDFplot=TRUE,
                  Rplot=TRUE,
                  cores=3,
                  saveStepresults=TRUE)

Arguments

runload	If champ.load() should be run? (default = TRUE)
directory	The folder directory of .idat files. (default = getwd())
filters	A character vector indicates filters should be done if load data from .idat files. You can remove some of the filters in it if you don't need that much. (default = c("XY","DetP","Beads","NoCG","SNP","MultiHit"))
runimpute	If champ.impute() should be run? Note that if your data contains too many NA, champ.impute() may remove not only CpGs, but also samples. (default = TRUE)
imputemethod	Which imputation method should be applied into champ.impute().
runQC	If champ.QC() should be run? (default = TRUE)
QCplots	A character vector indicates plots should be drawn by champ.QC(). You can remove some plots in it if you don't need them. (default = c("mdsPlot","densityPlot","dendrogram"))
runnorm	If champ.norm() should be run? (default = TRUE)
normalizationmethod	Which normalization method should be selected by champ.norm().
runSVD	If champ.SVD() should be run? (default = TRUE)
RGEffect	If Red Gree color Effect should be calculated in champ.SVD(). (default = FALSE)
runCombat	If champ.runCombat() should be run? (default = TRUE)
batchname	A character vector indicates what factors should be corrected by champ.runCombat(). (default = c("Slide"))
runDMP	If champ.DMP() should be run? (default = TRUE)
runDMR	If champ.DMR() should be run? (default = TRUE)
DMRmethod	Which DMR method should be applied by champ.DMR()? (default = TRUE)
runBlock	If champ.Block() should be run? (default = TRUE)
runGSEA	If champ.GSEA() should be run? (default = TRUE)
runEpiMod	If champ.EpiMod() should be run? (default = TRUE)
runCNA	If champ.CNA() should be run? (default = TRUE)
control	If champ.CNA() should be calculate copy number variance between case and control? (The other option for champ.CNA() is calculate copy number variance for each sample to the averaged value). (default = TRUE)
controlGroup	Which pheno should be treated as control group while running champ.CNA().(default = "champCtls")
runRefFree	If champ.reffree() should be run? (default = TRUE)
runRefBase	If champ.refbase() should be run? (default = TRUE)
compare.group	Which two phenos should be compared in champ.DMP()?
adjPVal	The adjusted p value for each function's significant cutoff.
resultsDir	The directory where result should be stored. (default = "./CHAMP_RESULT/")
arraytype	If the data set under analysis is "450K" or "EPIC"? (default = "450K")
PDFplot	If PDF files should be plotted during running? (default = TRUE)
Rplot	If R plots should be plotted during running? (default = TRUE)
cores	How many cores should be used for parallel running during champ.process()? (default = 3)
saveStepresults	If result of each steps should be saved as .rd file into resultsDir folder? (default = TRUE)

Value

CHAMP_RESULT

A list contains all results from each champ.method.

Author(s)

Yuan Tian

Examples

    ## Not run: 
        directory=system.file("extdata",package="ChAMPdata")
        champ.process(directory=directory)
        
## End(Not run)

JoshuaTian/MyChAMP documentation built on May 7, 2019, 12:04 p.m.