meffil.calculate.cnv: Calculate CNVs from IDAT files

In perishky/meffil: Efficient algorithms for DNA methylation

Calculate CNVs from IDAT files

Description

Based on the algorithm developed in R/CopyNumber450k bioconductor package

Usage

meffil.calculate.cnv(
  samplesheet,
  cnv.reference,
  chip = NA,
  verbose = FALSE,
  ...
)

Arguments

samplesheet	Output from meffil.create.samplesheet
cnv.reference	Name returned by meffil.list.cnv.references().
chip	Name returned by meffil.list.chips() (Default: NA).
verbose	Default = FALSE
...	Extra parameters to be passed to DNAcopy for segmentation. See details.

Details

The following default values are being used:

• trim = 0.1

• min.width = 5

• nperm = 10000

• alpha = 0.001

• undo.splits = "sdundo"

• undo.SD = 2

Value

Dataframe of segmented results

perishky/meffil documentation built on March 20, 2024, 1:56 a.m.