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### R code from vignette source 'acnr.Rnw'
### Encoding: UTF-8
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### code chunk number 1: acnr.Rnw:22-23
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library(acnr)
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### code chunk number 2: acnr.Rnw:29-48
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tf <- .5
dataSets <- c("GSE29172", "GSE11976")
regList <- lapply(dataSets, FUN=function(ds) {
regDat <- loadCnRegionData(dataSet=ds, tumorFraction=tf)
regs <- regDat[["region"]]
})
names(regList) <- dataSets
allregs <- unique(unlist(regList))
tab <- sapply(allregs, FUN=function(reg) {
sapply(regList, FUN=function(rr) sum(rr==reg))
})
cap <- paste("Size of annotated copy-number regions for each of the",
length(dataSets), "data sets.")
if (require(xtable)) {
print(xtable(tab, caption=cap, label="tab:regData",
table.placement="!h", caption.placement="bottom"))
}
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### code chunk number 3: acnr.Rnw:52-53
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sessionInfo()
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