slSummarization {cn.farms} | R Documentation

## Method for computation of the single-locus summarization

### Description

The different probes of the SNPs of the array are summarized to a probeset.

### Usage

    slSummarization(object, summaryMethod = "Exact", summaryParam = list(),
      callParam = list(runtype = "ff", cores = 1), summaryWindow = c("std",
      "fragment"), returnValues, saveFile = "slData")

### Arguments

`object` | An instance of `ExpressionSet`
`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.
`summaryWindow` | Method for combination of the SNPs. Possible values are sl and fragment.
`returnValues` | List with return values.
`saveFile` | Name of the file to save.

### Value

Single-locus summarized data of an instance of `ExpressionSet`

### Author(s)

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

### See Also

`summarizeFarmsExact`

### Examples

    load(system.file("exampleData/normData.RData", package = "cn.farms"))
    notes(experimentData(normData))$annotDir <-
            system.file("exampleData/annotation/pd.genomewidesnp.6/1.1.0",
                    package = "cn.farms")
    summaryMethod <- "Variational"
    summaryParam <- list()
    summaryParam$cyc <- c(10)
    slData <- slSummarization(normData,
            summaryMethod = summaryMethod,
            summaryParam = summaryParam)
    assayData(slData)$L_z[1:10, 1:10]

    summaryMethod <- "Gaussian"
    summaryParam <- list()
    summaryParam$cyc <- c(10)
    slData <- slSummarization(normData,
            summaryMethod = summaryMethod,
            summaryParam = summaryParam)
    assayData(slData)$L_z[1:10, 1:10]

    summaryMethod <- "Exact"
    summaryParam <- list()
    summaryParam$cyc <- c(10, 20)
    slData <- slSummarization(normData,
            summaryMethod = summaryMethod,
            summaryParam = summaryParam)
    assayData(slData)$L_z[1:10, 1:10]

[Package cn.farms version 1.42.0 Index]