dist.xyz. bio3d 2.3-0

Usage

dist.xyz(a, b = NULL, all.pairs=TRUE, ncore=1, nseg.scale=1)

Arguments

a: a ‘xyz’ object, numeric data matrix, or vector.
b: an optional second ‘xyz’ object, data matrix, or vector.
all.pairs: logical, if TRUE all pairwise distances between the rows of ‘a’ and all rows of ‘b’ are computed, if FALSE only the distances between coresponding rows of ‘a’ and ‘b’ are computed.
ncore: number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale: split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

Description

Compute the pairwise euclidean distances between the rows of two matrices.

Details

This function returns a matrix of euclidean distances between each row of ‘a’ and all rows of ‘b’. Input vectors are coerced to three dimensional matrices (representing the Cartesian coordinates x, y and z) prior to distance computation. If ‘b’ is not provided then the pairwise distances between all rows of ‘a’ are computed.

Value

Returns a matrix of pairwise euclidean distances between each row of ‘a’ and all rows of ‘b’.

References

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

Note

This function will choke if ‘b’ has too many rows.

Examples

 dist.xyz( c(1,1,1, 3,3,3), c(3,3,3, 2,2,2, 1,1,1))

         [,1]     [,2]     [,3]
[1,] 3.464102 1.732051 0.000000
[2,] 0.000000 1.732051 3.464102

 dist.xyz( c(1,1,1, 3,3,3), c(3,3,3, 2,2,2, 1,1,1), all.pairs=FALSE)

[1] 3.464102 1.732051       NA

Author

Barry Grant

Calculate the Distances Between the Rows of Two Matrices