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

methyl_master_epicopy

R Documentation

methyl_master_epicopy

Description

MethyMaster version of Epicopy::epicopy() function Epicopy by: Sean, Soonweng Cho, Hyunseok Kim and Leslie Cope (2017). Epicopy: Get CNVinformation from 450K array. R package version 0.99.0.

Usage

methyl_master_epicopy(
  epi.input.dir,
  epi.output.dir,
  epi.single.file,
  epi.single.file.path,
  epic.manifest.path,
  epi.reference.group,
  epi.comparison,
  epi.ncores,
  epi.ref,
  epi.normals,
  epi.samp.names,
  epi.qn,
  epi.mode.bw,
  epi.mode.method,
  epi.normal.cnv,
  epi.mean.center,
  epi.filter.probes,
  epi.retained.probes,
  epi.keepfnobj,
  epi.fn.output,
  epi.run.gistic = FALSE,
  ...
)

Arguments

`epi.input.dir`	The idat input dir
`epi.output.dir`	The output dir for epicopy functionality
`epi.single.file`	Whether a single file is used
`epi.single.file.path`	The single file path
`epic.manifest.path`	The EPIC manifest file path
`epi.reference.group`	The reference group to use
`epi.comparison`	The MehtylMaster comparison vector sheet
`epi.ncores`	The number of cores to use, multiple cores may not be supported on all systems
`epi.ref`	The Epicopy ref to use
`epi.normals`	The Epciopy normals to specify
`epi.samp.names`	The Epicopy sample names can be custom specified here
`epi.qn`	The Epicopy qn parameter
`epi.mode.bw`	The Epicopy mode.bw parameter
`epi.mode.method`	The Epicopy mode.method parameter
`epi.normal.cnv`	The Epicopy normal.cnv parameter
`epi.mean.center`	Whether to perform Epicopy mean centering
`epi.filter.probes`	The Epicopy filter.probes parameter
`epi.retained.probes`	The Epicopy retained probes parameter
`epi.keepfnobj`	The Epicopy keepfnobj parameter
`epi.fn.output`	The Epicopy fn.output parameter
`epi.run.gistic`	The Epicopy run.gistic parameter (Whetehr to run GISTIC)