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#line 37 "vignettes/cn.farms/inst/doc/cn.farms.Rnw"
options(width = 80)
set.seed(0)
library(cn.farms)
farmsVers <- packageDescription("cn.farms")$Version

##  toy-data which is used for testing the vignette
load(system.file("exampleData/normData.RData", package="cn.farms"))
load(system.file("exampleData/slData.RData", package="cn.farms"))
experimentData(normData)@other$annotDir <- 
		system.file("exampleData/annotation/pd.genomewidesnp.6/1.1.0",
				package="cn.farms")
cores <- 1
runtype <- "ff"
npData <- slData


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#line 292 "vignettes/cn.farms/inst/doc/cn.farms.Rnw"
summaryMethod <- "Variational"
summaryParam <- list()
summaryParam$cyc <- c(10)
callParam <- list(cores = cores, runtype = runtype)

slData <- slSummarization(normData, 
		summaryMethod = summaryMethod, 
		summaryParam = summaryParam,
		callParam = callParam,
		summaryWindow = "std")

show(slData)
assayData(slData)$intensity[1:10, 1:5] ## intensity values
assayData(slData)$L_z[1:10, 1:5] ## relative values


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#line 322 "vignettes/cn.farms/inst/doc/cn.farms.Rnw"
combData <- combineData(slData, npData, runtype = runtype)
show(combData) 


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#line 345 "vignettes/cn.farms/inst/doc/cn.farms.Rnw"
windowMethod <- "std"
windowParam <- list()
windowParam$windowSize <- 5
windowParam$overlap <- TRUE
summaryMethod <- "Variational"
summaryParam <- list()
summaryParam$cyc <- c(20)
callParam <- list(cores = cores, runtype = runtype)
mlData <- mlSummarization(slData, 
		windowMethod  = windowMethod, 
		windowParam   = windowParam, 
		summaryMethod = summaryMethod, 
		summaryParam  = summaryParam, 
		callParam     = callParam)
names(assayData(mlData))
assayData(mlData)$intensity[1:10, 1:5]
assayData(mlData)$L_z[1:10, 1:5]


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#line 369 "vignettes/cn.farms/inst/doc/cn.farms.Rnw"
colnames(assayData(mlData)$L_z) <- sampleNames(mlData)
segments <- dnaCopySf(
		x         = assayData(mlData)$L_z[, 1:10], 
		chrom     = featureData(mlData)@data$chrom, 
		maploc    = featureData(mlData)@data$start, 
		cores     = cores, 
		smoothing = FALSE)
head(featureData(segments)@data)


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#line 402 "vignettes/cn.farms/inst/doc/cn.farms.Rnw"
sessionInfo()