cnSegmentation {sesame}

R Documentation

Perform copy number segmentation

Description

Perform copy number segmentation using the signals in the signal set. The function takes a SigDF for the target sample and a set of normal SigDF 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(sdf, sdfs.normal = NULL, refversion = c("hg19", "hg38"))

Arguments

sdf	SigDF
sdfs.normal	a list of SigDFs for normalization, if not given, use the stored normal data from sesameData. However, we do recommend using a matched copy number normal dataset for normalization.
refversion	hg19 or hg38

Value

an object of CNSegment

Examples

sesameDataCache("EPIC") # in case not done yet
sdf <- sesameDataGet('EPIC.1.SigDF')
sdfs.normal <- sesameDataGet('EPIC.5.SigDF.normal')[1:3]
seg <- cnSegmentation(sdf, sdfs.normal)

# release memory for Windows package builder
rm(list=ls(env=sesameData:::cacheEnv), envir=sesameData:::cacheEnv)
gc()

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