LRRtoCNA: Convert LRR to segmented copy number

In sean-cho/Epicopy: Get CNV information from 450K array

Description

LRRtoCNA Converts LRR to segmented copy number using the circular binart segmentation (CBS) algorithm.

Usage

LRRtoCNA(LRR, sampID = NULL, ncores = 1L, seg.undo.splits = "sdundo",
  seg.undo.SD = 2, ...)

Arguments

LRR	Matrix of LRR from getLRR
sampID	Sample IDs. Default: NULL, uses colnames(LRR)
ncores	Integer. Default: 1L. Define number of cores for parallel segmentation. See details.
seg.undo.splits	Undo.splits argument for segment from DNAcopy. Default: 'sdundo'.
seg.undo.SD	undo.SD argument for segment. Default: 2.
...	Passes arguments to segment.

Details

This function coerces the LRR file into a suitable input for the CNA, smooth.CNA, and segment algorithm provided by the DNAcopy package. Parallelization for segmentation of ParDNAcopy package is implemented when ncores >= 2L.

Value

A segmented DNAcopy object. See segment.

See Also

CNA smooth.CNA segment parSegment

Examples

# Load example data
data(data_vignette)
# Run segmentation
epi_cna <- LRRtoCNA(epi_lrr, seg.undo.splits = 'sdundo', seg.undo.SD = 2)

sean-cho/Epicopy documentation built on May 29, 2019, 4:24 p.m.