champ.process.mm: champ.process.mm
In mmariani123/MethylMasteR: What the Package Does (One Line, Title Case)

View source: R/methyl_master_champ_helper_functions.R

champ.process.mm

R Documentation

champ.process.mm

Description

MethylMaster modified champ.process() function from ChAMP ChAMP by: #' Tian Y, Morris TJ, Webster AP, Yang Z, Beck S, Andrew F, Teschendorff AE (2017). "ChAMP: updated methylation analysis pipeline for Illumina BeadChips." Bioinformatics, btx513. doi: 10.1093/bioinformatics/btx513 (URL: https://doi.org/10.1093/bioinformatics/btx513).

Morris TJ, Butcher LM, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S (2014). "ChAMP: 450k Chip Analysis Methylation Pipeline." Bioinformatics, 30(3), 428-430. doi: 10.1093/bioinformatics/btt684 (URL: https://doi.org/10.1093/bioinformatics/btt684).

champ.lasso method is described in:

Butcher LM, Beck S (2015). "Probe Lasso: A novel method to rope in differentially methylated regions with 450K DNA methylation data." Methods, 72, 21-28. doi: 10.1016%2Fj.ymeth.2014.10.036 (URL: https://doi.org/10.1016%2Fj.ymeth.2014.10.036).

Usage

champ.process.mm(
  runload = TRUE,
  directory = getwd(),
  resultsDir = "./CHAMP_RESULT/",
  sample.sheet = NULL,
  arraytype = "450K",
  controlGroup = "champCtls",
  filters = c("XY", "DetP", "Beads", "NoCG", "SNP", "MultiHit"),
  runimpute = TRUE,
  imputemethod = "Combine",
  runQC = TRUE,
  QCplots = c("mdsPlot", "densityPlot", "dendrogram"),
  runnorm = TRUE,
  normalizationmethod = "BMIQ",
  runSVD = TRUE,
  RGEffect = FALSE,
  runCombat = TRUE,
  batchname = c("Slide"),
  runDMP = TRUE,
  runDMR = TRUE,
  DMRmethod = "Bumphunter",
  runBlock = TRUE,
  runGSEA = TRUE,
  runEpiMod = TRUE,
  runCNA = TRUE,
  control = TRUE,
  runRefBase = FALSE,
  compare.group = NULL,
  adjPVal = 0.05,
  PDFplot = TRUE,
  Rplot = TRUE,
  cores = 1,
  saveStepresults = TRUE
)

Arguments

`runload`	Whether to run runload
`directory`	Input directory for ChAMP
`resultsDir`	The Champ results directory, can be different from the output directory if desired
`sample.sheet`	The MethylMaster sample sheet path
`arraytype`	The arrray type, default "450k"
`controlGroup`	Specify the control Group
`filters`	Filters to use
`runimpute`	Whether to run imputation
`imputemethod`	The imputation method to use
`runQC`	Whether to run QC
`QCplots`	The QC plots to output
`runnorm`	Whether to run runnorm
`normalizationmethod`	The normalization method to use
`runSVD`	Whether to run SVD
`RGEffect`	The RGE effect logical
`runCombat`	Whether to run Combat batch correction
`batchname`	The name of the batch field in the MethylMaster sample sheet
`runDMP`	Whether to run DMP
`runDMR`	whether to run DMR
`DMRmethod`	The DMR method to use
`runBlock`	Whether to tun runBlock
`runGSEA`	Whether to run runGSEA
`runEpiMod`	Whether to run runEpiMod
`runCNA`	Whether to run runCNA
`control`	Whether or not to use control
`runRefBase`	Whether to run runRefBase
`compare.group`	The two-element MethylMaster comparison vector
`adjPVal`	The padj value to filter ChAMP results by
`PDFplot`	Whether to do PDF plots
`Rplot`	Whether to do R plots
`cores`	Number of cores to use, note that more than 1 core may not work on all systems.
`saveStepresults`	Whether to save the Stepresults