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

methyl_master

R Documentation

methyl_master

Description

MethyMaster main function: CNV calling platform from methylation data algorithms and additional comparison functionality Michael Mariani PhD Dartmouth College 2021-2022 Possible routines: "test" ##Run a quick test "process_sesame", ##Preprocess the TCGA and cord data in sesame format "sesame", ##Run Sesame CNV calling (get segments) "hm450" , ##Run 450K CNV calling (get segments) "champ" , ##Run ChAMP CNV calling (get segments) "epicopy" , ##Run EpiCopy CNV calling (get segments) "compare" ##Run algorithm comparison functionality

Usage

methyl_master(
  input.dir = NULL,
  output.dir = NULL,
  sample.sheet.path = NULL,
  file.sep = "/",
  r.lib.path = .libPaths()[1],
  n.cores = 1,
  os.type = "linux",
  proj = "TCGA-BLCA",
  visualize = FALSE,
  visualize.individual = FALSE,
  simplify.reduce = weightedmean,
  routine = "test",
  reference = NULL,
  reference.name = "all",
  split.by = NULL,
  comparison = NULL,
  form.thresholds = NULL,
  overlap.density = 0.1,
  sesame.data.cache = "EPIC",
  sesame.data.normal = "EPIC.5.normal",
  genome.version = "hg38",
  hm450.workflow = "B",
  champ.padj = 0.05,
  champ.control = FALSE,
  champ.run.combat = TRUE,
  champ.run.dmp = TRUE,
  champ.run.dmr = TRUE,
  champ.run.block = TRUE,
  champ.run.gsea = TRUE,
  champ.run.epimod = TRUE,
  epi.run.gistic = FALSE,
  compare.name = NULL,
  save.seg = FALSE,
  olaps.split.field = "Sample_ID",
  estimate.recurrence = FALSE,
  ov.less.stringent.ra.setting = ov.less.stringent.ra.setting,
  ov.pvalue = ov.pvalue,
  ov.keep.extra.columns = TRUE,
  ov.simplify.reduce = weightedmean,
  create.dir = FALSE,
  compare.list.files = FALSE,
  compare.files.in = NULL,
  compare.names = NULL,
  compare.olaps.size = 1,
  ...
)

Arguments

`input.dir`	Input directory
`output.dir`	Output directory
`sample.sheet.path`	Path to sample sheet
`file.sep`	File separator
`r.lib.path`	Path to r library default is .libPaths()
`n.cores`	Number of cores to run
`os.type`	The os type running the software
`proj`	The project name
`visualize`	Visualize the output
`visualize.individual`	Visualize individual sample plots for sesame
`simplify.reduce`	The reduction function being applied to the output
`routine`	The specific routine to run
`reference`	The reference to use
`reference.name`	The reference name, for the epicopy routine
`split.by`	Which additional metadata column to split the analysis by
`comparison`	Which groups from the metadata "Sample_Group" to compare
`form.thresholds`	The thresholds for cnv state calling
`overlap.density`	The overlap density applied to final results from the modified population ranges function
`sesame.data.cache`	The sesame data cache to use
`sesame.data.normal`	Which sesame normal data to use e.g."EPIC.5.Normal"
`genome.version`	The genome version
`hm450.workflow`	which hm450 workflow to use with the hm450 routine: "A", "B", or "C"
`champ.padj`	adjusted p-value threshold for the ChAMP routine
`champ.control`	select the champ control to use
`champ.run.combat`	run combat batch correction in the champ routine
`champ.run.dmp`	run dmp in the champ routin
`champ.run.dmr`	run dmr in the champ routine
`champ.run.block`	run block in the champ routine
`champ.run.gsea`	run gsea in the champ routine
`champ.run.epimod`	run epimod in the champ routine
`epi.run.gistic`	run GISTIC in the epicopy routine
`compare.name`	the compare.name to use
`save.seg`	whether to save the seg output or not
`olaps.split.field`	which field in the olaps to split the results by the default (recommended) is to use "Sample_ID"
`estimate.recurrence`	whether to use the estimate.recurrence feature in populationsRanges when looking at overlaps within a particular routine
`ov.less.stringent.ra.setting`	whether to use less stringent method when comparing overlaps of cnvs from an individual routine
`ov.pvalue`	the pvalue cutoff to use within a routine
`ov.keep.extra.columns`	whether to keep extra meta data columns or not when collating results from an individual routine
`ov.simplify.reduce`	which reduction method to use to compare overlaps within a routine
`create.dir`	create output directory when running MethylMaster, if already exists it will be over-written
`compare.list.files`	whether to list the files individually to be compared with the compare routine or not, otherwise will search through the input.dir path
`compare.files.in`	vector of file paths to individual routine results to use with the compare routine
`compare.names`	the names of the files (with paths) to run with the compare routine
`compare.olaps.size`	the overlaps size to use when considering an overlap hit across multiple routine results (using the compare routin)
`...`	additional parameters to be passed to methyl_master