beadarraySNP (version 1.38.0)

segmentate: Segmentation for SnpSetIllumina objects

Description

Use snapCGH package to perform segmentation

Usage

segmentate(object, method = c("DNACopy", "HMM", "BioHMM", "GLAD"), normalizedTo = 2, doLog = TRUE, doMerge = FALSE, useLair = FALSE, subsample = "OPA", alpha = 0.01)

Arguments

object

class SnpSetIllumina

method

char, type of segmentation

normalizedTo

numeric

doLog

logical, perform transformation before segmentation, see convert2seglist

doMerge

logical, perform merging of close states

useLair

logical, Also segmentate on lair

subsample

factor

alpha

numeric, probability threshold to distinguish segments

Value

SnpSetIllumina object with elements observed, states and predicted set in the AssayData slot