meffil.normalize.dataset: Functional normalization
In perishky/meffil: Efficient algorithms for DNA methylation

meffil.normalize.dataset

R Documentation

Functional normalization

Description

Apply functional normalization to a set of Infinium HumanMethylation450 BeadChip IDAT files.

Usage

meffil.normalize.dataset(
  samplesheet,
  number.quantiles = 500,
  detection.threshold = 0.01,
  bead.threshold = 3,
  sex.cutoff = -2,
  chip = NA,
  featureset = chip,
  cell.type.reference = NA,
  qc.parameters = meffil.qc.parameters(),
  qc.file = "meffil-qc-report.md",
  author = "Analyst",
  study = "IlluminaHuman450 data",
  number.pcs = 2,
  fixed.effects = NULL,
  random.effects = NULL,
  pseudo = 100,
  dup.fun = function(x) median(x, na.rm = T),
  just.beta = T,
  gds.filename = NULL,
  probe.range = 5000,
  autosomal = T,
  norm.parameters = NULL,
  norm.file = "meffil-normalization-report.md",
  verbose = FALSE
)

Arguments

`samplesheet`	Output from `meffil.read.samplesheet()` or `meffil.create.samplesheet()`. Arguments to `meffil.qc()`:
`cell.type.reference`	Argument to `meffil.qc.summary()`:
`qc.parameters`	(parameters) Arguments to `meffil.qc.report()`:
`qc.file`	(output.file)
`study`	Arguments to `meffil.normalize.quantiles()`:
`fixed.effects`	Names of columns in samplesheet that should be included as fixed effects along with control matrix principal components (Default: NULL).
`random.effects`	Names of columns in samplesheet that should be included as random effects (Default: NULL). Arguments to `meffil.normalize.samples()`:
`pseudo`	Arguments to `meffil.methylation.pcs()`.
`dup.fun`	Function to collapse duplicate probes (EPIC v2 has over 5000 duplicated probes). If NULL, then duplicates are not collapsed (Default: median).
`gds.filename`	If not `NULL` (default), then saves the output to a GDS (Genomic Data Structure). This is for cases where the output is too large to fit into main memory. The GDS option assumes that argument `just.beta == TRUE`.
`probe.range`	(Default: 5000).
`autosomal`	(Default: TRUE). Arguments to `meffil.normalization.summary()`:
`norm.parameters`	(parameters)
`norm.file`	(output.file) Other:
`verbose`	If `TRUE`, then status messages are printed during execution (Default: `FALSE`).
`npcs`	(Default: 1:10).

Details

Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD. Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biol. 2014 Dec 3;15(12):503. doi: 10.1186/s13059-014-0503-2. PMID: 25599564