segmentate {beadarraySNP} | R Documentation

## 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

### Author(s)

Jan Oosting

[Package beadarraySNP version 1.46.0 Index]