meffil.normalize.quantiles: Normalize microarray quantiles

In perishky/meffil: Efficient algorithms for DNA methylation

Normalize microarray quantiles

Description

Normalize microarray quantiles using controls extracted (Infinium HumanMethylation450 BeadChip).

Usage

meffil.normalize.quantiles(
  qc.objects,
  number.pcs = 2,
  fixed.effects = NULL,
  random.effects = NULL,
  verbose = F
)

Arguments

qc.objects	A list of outputs from meffil.create.qc.object().
number.pcs	Number of control matrix principal components to adjust for (Default: 2).
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).
verbose	If TRUE, then status messages are printed during execution (Default: FALSE).

Value

Same list as input with additional elements added for each sample including normalized quantiles needed for normalizing each sample.

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