NChannelSetToMethyLumiSet2: For internal use, is read using minfi-like machinery and then...

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

For internal use, is read using minfi-like machinery and then preprocessed into the more flexible and convenient methylumi object used by wateRmelon/bigmelon

Description

For internal use, is read using minfi-like machinery and then preprocessed into the more flexible and convenient methylumi object used by wateRmelon/bigmelon

Usage

NChannelSetToMethyLumiSet2(
  NChannelSet,
  parallel = F,
  pval = 0.05,
  n = F,
  n.sd = F,
  oob = T,
  to = TRUE
)

Arguments

NChannelSet	an NChannelSet (raw red and green values not yet mapped to Illumina IDs/CpG names
parallel	no effect, included for future parallelisation
pval	detection pval threshold for filtering. Inactivated.
n	keep nbeads data (min of m & u)
n.sd	process SD of U and M (not currently implemented)
oob	keep out-of-band signals
to	does chip have type I and II probes?

Value

A methylumi object with betas, U and M, optionally additional data

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.