meffil.add.cnv.reference: Create a copy number reference object

In perishky/meffil: Efficient algorithms for DNA methylation

Create a copy number reference object

Description

Create a copy number reference object for estimating copy number variation with the Infinium HumanMethylation450 BeadChip.

Usage

meffil.add.cnv.reference(
  name,
  M,
  U,
  chip = NA,
  featureset = chip,
  object = NULL,
  verbose = T
)

Arguments

name	Character string providing the name of the reference.
M	Matrix of methylated probe intensities (rows=CpG sites, columns=samples).
U	Matrix of unmethylatd probe intensities (rows=CpG sites, columns=samples).
chip	Name returned by meffil.list.chips() (Default: NA).
featureset	Name returned by meffil.list.featuresets() (Default: chip).
object	A previously created copy number reference object created by this function. If not NULL, then this reference is added with the given name and all other function arguments are ignored (Default: NULL).
verbose	If TRUE, then status messages are printed during execution (Default: FALSE).

Value

A list specifying a copy number reference object that can be used by meffil.calculate.cnv() to estimate copy number variation in another dataset.

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