cn.farms (version 1.20.0)

mlSummarization: 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

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)