meffil.calculate.cnv: Calculate CNVs from IDAT files

View source: R/cnv.r

meffil.calculate.cnvR Documentation

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 June 9, 2024, 5:59 p.m.