methyl_master_champ: methyl_master_champ
In mmariani123/MethylMasteR: What the Package Does (One Line, Title Case)

methyl_master_champ

R Documentation

methyl_master_champ

Description

My function to call the ChAMP::champ.process() function For ChAMP refs see: 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

methyl_master_champ(
  champ.input.dir = getwd(),
  champ.output.dir = getwd(),
  champ.sample.sheet = NULL,
  champ.array.type = "hm450",
  champ.batch.name = c("batch"),
  champ.padj = 0.05,
  champ.ncores = 1,
  champ.control = TRUE,
  champ.control.group = "normal",
  champ.comparison = c("tumor", "normal"),
  champ.split.by = NULL,
  champ.runimpute = TRUE,
  champ.runQC = TRUE,
  champ.runnorm = TRUE,
  champ.runSVD = TRUE,
  champ.runCombat = TRUE,
  champ.runDMP = TRUE,
  champ.runDMR = TRUE,
  champ.runBlock = TRUE,
  champ.runGSEA = TRUE,
  champ.runEpiMod = TRUE,
  ...
)

Arguments

`champ.input.dir`	The input idat files dir
`champ.output.dir`	The output dir for ChAMP output files
`champ.sample.sheet`	The MethylMaster sample sheet path
`champ.array.type`	The array type being used, default is "hm450"
`champ.batch.name`	The field in the sample sheet used as batch field for batch correction with combat, default is c("Batch")
`champ.padj`	The p.adj value to filter ChAMP result by (default is 0.05)
`champ.ncores`	The number of cores to use with ChAMP, note that more than 1, i.e. parallel processing, may not work on all systems.
`champ.control`	The champ control to use
`champ.control.group`	The specific ChAMP control group
`champ.comparison`	The MethylMaster comparison 2 element vector
`champ.runimpute`	Whether to run Champ.runimpute or not
`champ.runQC`	Whether to run champ.runQC or not
`champ.runnorm`	Whether to run champ.runnorm or not
`champ.runSVD`	Whether to run champ.runSVD or not
`champ.runCombat`	Whether to run combat in champ (champ.runCombat)
`champ.runDMP`	Whether to run champ.runDMP
`champ.runDMR`	Whether to run champ.DMR
`champ.runBlock`	Whether to run champ.runBlock
`champ.runGSEA`	Whether to run champ.runGSEA
`champ.runEpiMod`	Whether to run champ.runEpiMod
`...`	Additional parameter to pass to ChAMP