bio3d (version 2.4-4)

bounds: Bounds of a Numeric Vector

Description

Find the ‘bounds’ (i.e. start, end and length) of consecutive numbers within a larger set of numbers in a given vector.

Usage

bounds(nums, dup.inds=FALSE, pre.sort=TRUE)

Value

Returns a three column matrix listing starts, ends and lengths.

Arguments

nums

a numeric vector.

dup.inds

logical, if TRUE the bounds of consecutive duplicated elements are returned.

pre.sort

logical, if TRUE the input vector is ordered prior to bounds determination.

Author

Barry Grant

Details

This is a simple utility function useful for summarizing the contents of a numeric vector. For example: find the start position, end position and lengths of secondary structure elements given a vector of residue numbers obtained from a DSSP secondary structure prediction.

By setting ‘dup.inds’ to TRUE then the indices of the first (start) and last (end) duplicated elements of the vector are returned. For example: find the indices of atoms belonging to a particular residue given a vector of residue numbers (see below).

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

 test <- c(seq(1,5,1),8,seq(10,15,1))
 bounds(test)

 test <- rep(c(1,2,4), times=c(2,3,4))
 bounds(test, dup.ind=TRUE)