### Aliases: class:ViewsList ViewsList-class ViewsList

### R code from vignette source '/Users/dtenenba/dev/bioc_devel/IRanges//vignettes/IRangesOverview.Rnw'
### code chunk number 2: biocLite (eval = FALSE)
### code chunk number 11: Rle-construction
### code chunk number 12: Rle-vector-compare
### code chunk number 19: list-construct
### code chunk number 22: list-groupgenerics
### code chunk number 23: list-endoapply
### code chunk number 24: iranges-constructor
### code chunk number 28: iranges-subset-numeric
### code chunk number 29: iranges-subset-logical
### code chunk number 30: ranges-extraction
### code chunk number 34: rangeslist-contructor
### code chunk number 35: rangeslist-start
### code chunk number 36: bracket-ranges
### code chunk number 37: overlap-ranges
### code chunk number 38: ranges-coverage
### code chunk number 41: ranges-asterisk
### code chunk number 43: ranges-threebands
### code chunk number 44: ranges-restrict
### code chunk number 45: ranges-disjoin
### code chunk number 46: ranges-disjointBins
### code chunk number 47: ranges-reflect
### code chunk number 53: ranges-intersect
### code chunk number 54: ranges-pintersect
### code chunk number 55: ranges-setdiff
### code chunk number 56: ranges-psetdiff
### code chunk number 57: Views-constructors
### code chunk number 59: RangedData-construct
### code chunk number 60: RangedData-construct-space
### code chunk number 61: RangedData-ranges
### code chunk number 62: RangedData-values
### code chunk number 63: RangedData-subspace
### code chunk number 64: RangedData-subspace-2
### code chunk number 65: RangedData-names
### code chunk number 66: RangedData-length
### code chunk number 67: RangedData-lapply
### code chunk number 68: RangedData-extract
### code chunk number 69: RangedData-dollar
### code chunk number 70: RangedData-subset-2d

yVector <- rpois(1e7, lambda[c(251:length(lambda), 1:250)])
xSnippet <- window(xVector, start = 4751, end = 4760)
aggregate(xSnippet, start = 1:8, width = 3, FUN = median)
corrs  <- shiftApply(shifts, yVector, xVector, FUN = cor)
shiftApply(249:251, yRle, xRle, FUN = function(x, y) var(x, y) / (sd(x) * sd(y)))
cIntList1 <- IntegerList(x = xVector, y = yVector)
sIntList2 <- IntegerList(x = xVector, y = yVector, compress = FALSE)
xExploded <- lapply(xVector[1:5000], function(x) seq_len(x))
sIntList2 <- IntegerList(xExploded, compress = FALSE)
xRleList <- RleList(xRle, 2L * rev(xRle))
yRleList <- RleList(yRle, 2L * rev(yRle))
safe.max <- function(x) { if(length(x)) max(x) else integer(0) }
ir1 <- IRanges(start = 1:10, width = 10:1)
identical(ir1, ir2) & identical(ir2, ir3)
plotRanges <- function(x, xlim = x, main = deparse(substitute(x)),
bins <- disjointBins(IRanges(start(x), end(x) + 1))
plot.window(xlim, c(0, max(bins)*(height + sep)))
ybottom <- bins * (sep + height) - height
rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = col, ...)
irextract <- IRanges(start = c(4501, 4901) , width = 100)
mat <- rbind(cbind(mat[d,1]+1, mat[d,2]), mat)
rd <- RangedData(ir, name = letters[seq_len(length(ir))], values)
rd <- RangedData(ir, name = letters[seq_len(length(ir))], values,
space = rep(c("chr1", "chr2"), c(3, length(ir) - 3)))