Process function to run all methods in ChAMP pipeline.

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

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    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

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

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