cn.farms (version 1.20.0)

combineData: Combine two ExpressionSet objects

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.

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