segmentate: Segmentation for SnpSetIllumina objects

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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

Author(s)

Jan Oosting

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.