89 lines
2.8 KiB
R
89 lines
2.8 KiB
R
|
## ----install, eval=FALSE------------------------------------------------------
|
||
|
|
# if (!require("BiocManager"))
|
||
|
|
# install.packages("BiocManager")
|
||
|
|
# BiocManager::install("S4Vectors")
|
||
|
|
|
||
|
|
## ----message=FALSE------------------------------------------------------------
|
||
|
|
library(S4Vectors)
|
||
|
|
|
||
|
|
## ----Rle-extends-Vector-------------------------------------------------------
|
||
|
|
showClass("Rle")
|
||
|
|
|
||
|
|
## ----initialize---------------------------------------------------------------
|
||
|
|
set.seed(0)
|
||
|
|
lambda <- c(rep(0.001, 4500), seq(0.001, 10, length=500),
|
||
|
|
seq(10, 0.001, length=500))
|
||
|
|
xVector <- rpois(1e7, lambda)
|
||
|
|
yVector <- rpois(1e7, lambda[c(251:length(lambda), 1:250)])
|
||
|
|
xRle <- Rle(xVector)
|
||
|
|
yRle <- Rle(yVector)
|
||
|
|
|
||
|
|
## ----basic-ops----------------------------------------------------------------
|
||
|
|
length(xRle)
|
||
|
|
xRle[1]
|
||
|
|
zRle <- c(xRle, yRle)
|
||
|
|
|
||
|
|
## ----seq-extraction-----------------------------------------------------------
|
||
|
|
xSnippet <- window(xRle, 4751, 4760)
|
||
|
|
xSnippet
|
||
|
|
head(xSnippet)
|
||
|
|
tail(xSnippet)
|
||
|
|
rev(xSnippet)
|
||
|
|
rep(xSnippet, 2)
|
||
|
|
subset(xSnippet, xSnippet >= 5L)
|
||
|
|
|
||
|
|
## ----seq-concatenate----------------------------------------------------------
|
||
|
|
c(xSnippet, rev(xSnippet))
|
||
|
|
append(xSnippet, xSnippet, after=3)
|
||
|
|
|
||
|
|
## ----aggregate----------------------------------------------------------------
|
||
|
|
xSnippet
|
||
|
|
aggregate(xSnippet, start=1:8, width=3, FUN=median)
|
||
|
|
|
||
|
|
## ----shiftApply-cor-----------------------------------------------------------
|
||
|
|
cor(xRle, yRle)
|
||
|
|
shifts <- seq(235, 265, by=3)
|
||
|
|
corrs <- shiftApply(shifts, yRle, xRle, FUN=cor)
|
||
|
|
|
||
|
|
## ----figshiftcorrs, eps=FALSE, fig.align='center', fig.cap='Correlation between `xRle` and `yRle` for various shifts'----
|
||
|
|
plot(shifts, corrs)
|
||
|
|
|
||
|
|
## ----Rle-vector-compare-------------------------------------------------------
|
||
|
|
as.vector(object.size(xRle) / object.size(xVector))
|
||
|
|
identical(as.vector(xRle), xVector)
|
||
|
|
|
||
|
|
## ----Rle-accessors------------------------------------------------------------
|
||
|
|
head(runValue(xRle))
|
||
|
|
head(runLength(xRle))
|
||
|
|
|
||
|
|
## ----Rle-ops------------------------------------------------------------------
|
||
|
|
xRle > 0
|
||
|
|
xRle + yRle
|
||
|
|
xRle > 0 | yRle > 0
|
||
|
|
|
||
|
|
## ----Rle-summary--------------------------------------------------------------
|
||
|
|
range(xRle)
|
||
|
|
sum(xRle > 0 | yRle > 0)
|
||
|
|
|
||
|
|
## ----Rle-math-----------------------------------------------------------------
|
||
|
|
log1p(xRle)
|
||
|
|
|
||
|
|
## ----Rle-cor------------------------------------------------------------------
|
||
|
|
cor(xRle, yRle)
|
||
|
|
shiftApply(249:251, yRle, xRle,
|
||
|
|
FUN=function(x, y) {var(x, y) / (sd(x) * sd(y))})
|
||
|
|
|
||
|
|
## ----DataFrame-extends-List---------------------------------------------------
|
||
|
|
showClass("DataFrame")
|
||
|
|
|
||
|
|
## ----DataFrame, warning=FALSE-------------------------------------------------
|
||
|
|
df <- DataFrame(x=xRle, y=yRle)
|
||
|
|
sapply(df, class)
|
||
|
|
sapply(df, summary)
|
||
|
|
sapply(as.data.frame(df), summary)
|
||
|
|
endoapply(df, `+`, 0.5)
|
||
|
|
|
||
|
|
## ----SessionInfo, echo=FALSE--------------------------------------------------
|
||
|
|
sessionInfo()
|
||
|
|
|