cnSegmentation: Perform copy number segmentation

In sesame: Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Description

Perform copy number segmentation using the signals in the signal set. The function takes a SigSet for the target sample and a set of normal SigSet for the normal samples. An optional arguments specifies the version of genome build that the inference will operate on. The function outputs an object of class CNSegment with signals for the segments ( seg.signals), the bin coordinates ( bin.coords) and bin signals (bin.signals).

Usage

cnSegmentation(sset, ssets.normal, refversion = c("hg19", "hg38"))

Arguments

sset	SigSet
ssets.normal	SigSet for normalization
refversion	hg19 or hg38

Value

an object of CNSegment

Examples

sset <- sesameDataGet('EPIC.1.LNCaP')$sset
ssets.normal <- sesameDataGet('EPIC.5.normal')
seg <- cnSegmentation(sset, ssets.normal)

sesame documentation built on Nov. 15, 2020, 2:08 a.m.