segmentize {rbamtools}R Documentation

Segmentation of vector using segment coordinates

Description

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

Usage

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

Arguments

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.

Details

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.

Value

Integer vector

Author(s)

Wolfgang Kaisers

Examples

# 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)
[Package rbamtools version 2.16.11.2 Index]