Nothing
## ---- include=FALSE------------------------------------------------------
library("jointseg")
## ---- include=FALSE------------------------------------------------------
library("knitr")
opts_chunk$set(dev='png', fig.width=5, fig.height=5)
opts_knit$set(eval.after = "fig.cap")
## ------------------------------------------------------------------------
citation("jointseg")
## ---- include=FALSE------------------------------------------------------
library("jointseg")
## ------------------------------------------------------------------------
n <- 1e4 ## signal length
bkp <- c(2334, 6121) ## breakpoint positions
regions <- c("(1,1)", "(1,2)", "(0,2)") ## copy number regions
## ------------------------------------------------------------------------
ylims <- cbind(c(0, 5), c(-0.1, 1.1))
colG <- rep("#88888855", n)
hetCol <- "#00000088"
## ------------------------------------------------------------------------
plotFUN <- function(dataSet, tumorFraction) {
regDat <- acnr::loadCnRegionData(dataSet=dataSet, tumorFraction=tumorFraction)
sim <- getCopyNumberDataByResampling(n, bkp=bkp,
regions=regions, regData=regDat)
dat <- sim$profile
wHet <- which(dat$genotype==1/2)
colGG <- colG
colGG[wHet] <- hetCol
plotSeg(dat, sim$bkp, col=colGG)
}
## ------------------------------------------------------------------------
ds <- "GSE29172"
## ---- fig.cap=paste("Data set", ds, ":", pct, "% tumor cells")-----------
pct <- 1
plotFUN(ds, pct)
## ---- fig.cap=paste("Data set", ds, ":", pct, "% tumor cells (another resampling)")----
plotFUN(ds, pct)
## ---- fig.cap=paste("Data set", ds, ":", pct, "% tumor cells")-----------
pct <- 0.7
plotFUN(ds, pct)
## ---- fig.cap=paste("Data set", ds, ":", pct, "% tumor cells")-----------
pct <- 0.5
plotFUN(ds, pct)
## ------------------------------------------------------------------------
ds <- "GSE11976"
## ------------------------------------------------------------------------
sessionInfo()
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