slSummarization: Method for computation of the single-locus summarization

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

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

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]

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