cn.farms (version 1.20.0)

slSummarization: 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

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]