mlSummarization: Method for computation of the multi-loci summarization

In cn.farms: cn.FARMS - factor analysis for copy number estimation

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 [e-mail] and Andreas Mitterecker [e-mail]

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)

cn.farms documentation built on Nov. 8, 2020, 7:59 p.m.