meffil.qc: Perform QC on HumanMethylation450 idat files

View source: R/qc.r

meffil.qcR 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).

Value

List containing control probe information, probe summaries and quantiles.


perishky/meffil documentation built on June 9, 2024, 5:59 p.m.