meffil.create.qc.object: Quality control object

In perishky/meffil: Efficient algorithms for DNA methylation

Quality control object

Description

Create a quality control object for a given Infinium HumanMethylation450 BeadChip.

Usage

meffil.create.qc.object(
  samplesheet.row,
  number.quantiles = 500,
  dye.intensity = 5000,
  verbose = F,
  detection.threshold = 0.01,
  bead.threshold = 3,
  sex.cutoff = -2,
  chip = NA,
  featureset = chip,
  cell.type.reference = NA
)

Arguments

samplesheet.row	Row from the data frame containing IDAT file and sample info (see meffil.read.samplesheet or 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).
verbose	If TRUE, then status messages are printed during execution (Default: FALSE).
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().

Value

List containing control probe information, probe summaries and quantiles. We call this a "QC object".

perishky/meffil documentation built on March 20, 2024, 1:56 a.m.