meffil.qc: Perform QC on HumanMethylation450 idat files
In perishky/meffil: Efficient algorithms for DNA methylation

meffil.qc

R Documentation

Perform QC on HumanMethylation450 idat files

Description

Read in control matrices for each sample. Perform background correction and R/G dye bias correction. Predict sex

Usage

meffil.qc(
  samplesheet,
  number.quantiles = 500,
  dye.intensity = 5000,
  detection.threshold = 0.01,
  bead.threshold = 3,
  sex.cutoff = -2,
  chip = NA,
  featureset = chip,
  cell.type.reference = NA,
  max.bytes = 2^30 - 1,
  verbose = F,
  ...
)

Arguments

`samplesheet`	Data frame containing IDAT file and sample info (see `meffil.read.samplesheet` pr `meffil.create.samplesheet`).
`number.quantiles`	Number of quantiles to compute for probe subset (Default: 500).
`dye.intensity`	Reference intensity for scaling each color channel (Default: 5000).
`detection.threshold`	Default value = 0.01. All probes above this detection threshold detected.
`bead.threshold`	Default value = 3. All probes with less than this number of beads detected.
`sex.cutoff`	Sex prediction cutoff. Default value = -2.
`chip`	Name returned by `meffil.list.chips()` (Default: `NA`).
`featureset`	Name returned by `meffil.list.featuresets()` (Default: `chip`).
`cell.type.reference`	Character string name of the cell type reference to use for estimating cell counts. Estimates are not generated if set to NA (default). See `meffil.list.cell.type.references()` for a list of available references. New references can be created using `meffil.add.cell.type.reference()`.
`verbose`	If `TRUE`, then status messages are printed during execution (Default: `FALSE`).