combineData: Combine two ExpressionSet objects

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

Description

Suitable for SNP or non-polymorphic data which were already processed with single locus FARMS

Usage

combineData(object01, object02, obj01Var = "intensity",
  obj02Var = "intensity", runtype = "ff", saveFile = "combData")

Arguments

object01	An instance of ExpressionSet either with SNP or non-polymorphic data
object02	An instance of ExpressionSet either with SNP or non-polymorphic data
obj01Var	States the variable which should be combined from the assayData slot. Default is intensity.
obj02Var	States the variable which should be combined from the assayData slot. Default is intensity.
runtype	Mode how the results are saved. Possible values are ff or bm. If ff is chosen the data will not be saved automatically. With bm the results will be saved permanently.
saveFile	Name of the file to save.

Value

An instance of ExpressionSet.

Author(s)

Djork-Arne Clevert [e-mail] and Andreas Mitterecker [e-mail]

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, ]
combData <- combineData(slData, slData)
combData

mitterecker/cn.farms documentation built on March 10, 2020, 10:19 a.m.