meffil.normalize.samples: Normalize Infinium HumanMethylation450 BeadChips

In perishky/meffil: Efficient algorithms for DNA methylation

Normalize Infinium HumanMethylation450 BeadChips

Description

Normalize a set of samples using their normalized quality control objects.

Usage

meffil.normalize.samples(
  norm.objects,
  pseudo = 100,
  just.beta = T,
  cpglist.remove = NULL,
  remove.poor.signal = F,
  dup.fun = function(x) median(x, na.rm = T),
  max.bytes = 2^30 - 1,
  gds.filename = NULL,
  verbose = F,
  ...
)

Arguments

norm.objects	The list or sublist of meffil.normalize.quantiles().
pseudo	Value to add to the denominator to make the methylation estimate more stable when calculating methylation levels (Default: 100).
just.beta	If TRUE, then return just the normalized methylation levels; otherwise, return the normalized methylated and unmethylated matrices (Default: TRUE).
cpglist.remove	Optional list of CpGs to exclude from final output
remove.poor.signal	Set methylation values for poorly detected probes to missing (Default: FALSE). Poor signal was identified during QC by meffil.qc() as signal that failed to pass the detection p-value threshold (detection.threshold) or bead threshold (bead.threshold).
dup.fun	Function to collapse duplicate probes (EPIC v2 has over 5000 duplicated probes). If NULL, then duplicates are not collapsed (Default: median).
gds.filename	If not NULL (default), then saves the output to a GDS (Genomic Data Structure). This is for cases where the output is too large to fit into main memory. The GDS option assumes that argument just.beta == TRUE.
verbose	If TRUE, then detailed status messages are printed during execution (Default: FALSE).
...	Arguments passed to mclapply().

Value

If just.beta == TRUE, the normalized matrix of methylation levels between between 0 and 1 equal to methylated signal/(methylated + unmethylated signal + pseudo). Otherwise, a list containing two matrices, the normalized methylated and unmethylated signals. If gds.filename is not NULL, then the output is saved to the GDS file rather than retained in memory and returned to the caller. The library 'gdsfmt' must be installed in this case.

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