segmentize: Segmentation of vector using segment coordinates
In rbamtools: Read and Write BAM (Binary Alignment) Files

Description Usage Arguments Details Value Author(s) Examples

The function returns extracts of a data vector using two vector defining begin and end coordinates. An offset can be used.

1	segmentize(x, begin, end, offset=1, margin=1, invert=FALSE)

`x`	`numeric` object. Data vector from which segments are extracted.

begin

numeric object. Indices first segment elements.

end

numeric object. Indices of last segment elements. Length must be equal to length(begin). segmentize requires all(end>=begin).

offset

numeric object. The indices are shifted so that the first entry is indexed by value indicated by offset. Standard value is 1 (default behaviour in R).

margin

numeric object. Direction of segmentation for matrix and data.frame objects (1=rows, 2=columns).

invert

logical object. When TRUE, the complement of the selected segments is returned. Here, the ordering of the returned values cannot be changed.

The inversion option internally operates using logical values. As a consequence, when begin and end define overlapping regions, in effect the union of these regions is removed, because regions are only retained when they are not covered by any segment defined by begin and end.

Integer vector

Wolfgang Kaisers

# Create data vector
x <- rep(0, 11)
x[3:5] <- 1:3
x[7:9] <- 4:6
names(x) <- 10:20
# Define extracted segments
sgb <- c(3, 7)
sge <- c(5, 9)
sgm <- segmentize(x, sgb, sge)
names(sgm) <- segmentize(names(x), sgb, sge)
# Use offset
offset <- 10
sgb <- c(12, 16)
sge <- c(14, 18)
segmentize(x, sgb, sge, offset)
# Matrix
m <- matrix(0L, nrow=11, ncol=5)
rownames(m) <- 10:20
colnames(m) <- letters[1:5]

for(i in 1:5)
    m[c(3:5, 7:9), i] <- c(1:3, 4:6) * i
ms <- segmentize(m, sgb, sge, offset)