bounds {bio3d}

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)

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.

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).

Value

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

Author(s)

Barry Grant

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)