meffil.qc.parameters: Specify parameters for QC

In perishky/meffil: Efficient algorithms for DNA methylation

Specify parameters for QC

Description

Specify parameters for QC

Usage

meffil.qc.parameters(
  colour.code = NULL,
  control.categories = NULL,
  sex.outlier.sd = 3,
  meth.unmeth.outlier.sd = 3,
  control.means.outlier.sd = 5,
  detectionp.samples.threshold = 0.2,
  beadnum.samples.threshold = 0.2,
  detectionp.cpgs.threshold = 0.2,
  beadnum.cpgs.threshold = 0.2,
  snp.concordance.threshold = 0.9,
  sample.genotype.concordance.threshold = 0.9
)

Arguments

colour.code	Default value = NULL
control.categories	Default value = control.probe.categories()
sex.outlier.sd	Sets the standard deviation multiple at which sex outliers are identified. Default value = 3.
meth.unmeth.outlier.sd	Sets the standard deviation multiple at which methylated/unmethylated signal outliers are identified. Default value = 3.
control.means.outlier.sd	Sets the standard deviation multiple at which control probe signals are identified as outliers. Default value = 5
detectionp.samples.threshold	Maximum threshold on the fraction of undetected probes (probe detection is defined by setting the maximum probe detection p-value threshold parameter detection.threshold of meffil.qc() or meffil.normalize.dataset()). Samples with probe fractions above this will be excluded from the final dataset. Default value = 0.2
beadnum.samples.threshold	Maximum threshold on the fraction of probes with too few detected beads (minimum number of detected beads is defined by setting the beads.threshold parameter of meffil.qc() or meffil.normalize.dataset()). Samples with probe fractions above this will be excluded from the final dataset. Default value = 0.2
detectionp.cpgs.threshold	Same as detectionp.cpgs.threshold but used to identify poor quality probes in terms of the fraction of samples in which the probe is undetected. Default value = 0.2
beadnum.cpgs.threshold	Same as beadnum.samples.threshold but used to identify poor quality probes in terms of the fraction of samples in which the probe has too few detected beads. Default value = 0.2
snp.concordance.threshold	Minimum required concordance between supplied genotypes and genotypes estimated from a SNP probe. Default value = 0.99
sample.genotype.concordance.threshold	Minimum required concordance between supplied genotypes and genotypes estimated from SNP probes for a given individual. Default value = 0.9

Value

List of parameter values

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