mlSummarization {cn.farms} | R Documentation

## Method for computation of the multi-loci summarization

### Description

Method for computation of the multi-loci summarization

### Usage

    mlSummarization(object, windowMethod, windowParam, summaryMethod, summaryParam,
      callParam = list(runtype = "ff"), returnValues, saveFile = "mlData")

### Arguments

`object` | an instance of `ExpressionSet`
`windowMethod` | Method for combination of neighbouring SNPs. Possible values are Std and Bps.
`windowParam` | further parameters as the window size
`summaryMethod` | allowed versions for the summarization step are: Gaussian, Variational, Exact. Default is Variational.
`summaryParam` | The parameters for the summaryMethod. Further information can be obtained via the according functions: `cn.farms`, `cn.farms` or `cn.farms`
`callParam` | Additional parameters for runtype (ff or bm) as well as cores for parallelization.
`returnValues` | List with return values.
`saveFile` | Name of the file to save. For possible values see summaryMethod.

### Value

Multi-loci summarized data of an instance of `ExpressionSet`

### Author(s)

Djork-Arne Clevert okko@clevert.de and Andreas Mitterecker mitterecker@bioinf.jku.at

### Examples

    load(system.file("exampleData/slData.RData", package = "cn.farms"))
    windowMethod <- "std"
    windowParam <- list()
    windowParam$windowSize <- 5
    windowParam$overlap <- TRUE
    summaryMethod <- "Variational"
    summaryParam <- list()
    summaryParam$cyc <- c(20)
    mlData <- mlSummarization(slData, windowMethod, windowParam,
            summaryMethod, summaryParam)
    assayData(mlData)

[Package cn.farms version 1.40.0 Index]