Nothing
## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ---- message=FALSE------------------------------------------------------
library("acnr")
library("R.utils")
## ------------------------------------------------------------------------
dataSets <- listDataSets()
dataSet <- dataSets[2]
print(dataSet)
tfs <- listTumorFractions(dataSet)
tf <- tfs[1]
(tf)
dat <- loadCnRegionData(dataSet, tumorFraction=tf)
region <- as.factor(dat$region)
## ------------------------------------------------------------------------
x <- dat$c
rm(dat)
## ---- fig.width=4, fig.height=2, message=FALSE---------------------------
lim <- c(0, 0.05)
res <- sapply(levels(region), function (rr){
xTrue <- x[which(region==rr)]
xResamp <- sample(xTrue)
mar <- c(2, 2, 1, 0)+0.2
par(mar=mar)
acf(xTrue, ylim=lim)
mtext(sprintf("Original data: %s", rr), side=3)
acf(xResamp, ylim=lim)
mtext(sprintf("Resampled data: %s", rr), side=3)
})
## ---- results='asis'-----------------------------------------------------
tst <- "Ljung-Box"
lag <- 20
res <- sapply(levels(region), function (rr){
xTrue <- x[which(region==rr)]
len <- length(xTrue)
xResamp <- sample(xTrue)
bt <- Box.test(xTrue, lag=lag, type=tst)
br <- Box.test(xResamp, lag=lag, type=tst)
c("Original data"=bt$p.value, "Resampled data"=br$p.value, "Region size"=len)
})
cpt <- sprintf("$p$-values of the %s auto-correlation test (lag=%s)", tst, lag)
knitr::kable(t(res), caption=cpt)
## ------------------------------------------------------------------------
plot(sort(res[2, ]), ylab="p-value", xlab="rank", main="sorted p-values", pch=19, col=3, ylim=c(0,1))
points(sort(res[1, ]), pch=19, col=1)
abline(a=0, b=1/ncol(res), lty=2)
## ---- results='asis'-----------------------------------------------------
tst <- "Ljung-Box"
lag <- 20
maxSize <- 2000
res2 <- sapply(levels(region), function (rr){
xTrue <- head(x[which(region==rr)], maxSize)
len <- length(xTrue)
xResamp <- sample(xTrue)
bt <- Box.test(xTrue, lag=lag, type=tst)
br <- Box.test(xResamp, lag=lag, type=tst)
c("Original data"=bt$p.value, "Resampled data"=br$p.value, "Region size"=len)
})
cpt <- sprintf("$p$-values of the %s auto-correlation test (lag=%s) for regions of size <= %s", tst, lag, maxSize)
knitr::kable(t(res2), caption=cpt)
## ------------------------------------------------------------------------
plot(sort(res2[2, ]), ylab="p-value", xlab="rank", main="sorted p-values", pch=19, col=3, ylim=c(0,1))
points(sort(res2[1, ]), pch=19, col=1)
abline(a=0, b=1/ncol(res), lty=2)
## ------------------------------------------------------------------------
sessionInfo()
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