sdists {cba}R Documentation

Sequence Distance Computation

Description

This function computes and returns the auto-distance matrix between the vectors of a list or between the character strings of a vector treating them as sequences of symbols, as well as the cross-distance matrix between two such lists or vectors.

Usage

sdists(x, y = NULL, method = "ow", weight = c(1, 0, 2), 
                    exclude = c(NA,NaN,Inf,-Inf))

Arguments

x,y a list (of vectors) or a vector of character
method a mnemonic string referencing a distance measure
weight vector or matrix of parameter values
exclude argument to factor

Details

This function provides a common interface to different methods for computation of distances between sequences, such as the edit a.k.a. Levenshtein distance. Conversely, in the context of sequence alignment the similarity of the maximizing alignment is computed.

Note that negative similarities are returned as distances. So be careful to use a proper weighting (scoring) scheme.

The following methods are currently implemented:

ow:
operation-weight edit distance. Weights have to be specified for insertion/deletion, equality (match), and replacement.
aw:
alphabet-weight sequential alignment similarity. A matrix of weights (scores) for all possible symbol replacements needs to be specified with the convention that the first row/column defines the replacement with the empty (space) symbol. The colnames of this matrix are used as the levels argument when encoded by factor. Consequently, unspecified symbols are mapped to NA.
awl:
alphabet-weight local sequential alignment similarity. The weight matrix must be as described above.

Missing (non-finite) values should be avoided, i.e. either be removed or recoded (and appropriately weighted). By default they are excluded when coercing to factor and therfore mapped to NA. The result is then defined to be NA as we cannot determine a match!

The time complexity is O(n*m) for two sequences of length n and m.

Value

Auto distances are returned as an object of class dist and cross-distances as an object of class matrix.

Warning

The interface is experimental and may change in the future

Author(s)

Christian Buchta

References

D. Gusfield (1997) Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Chapter 11.

See Also

dists for compuation of common distances, agrep for searches for approximate matches.

Examples

### numeric data
sdists(list(c(2,2,3),c(2,4,3)))                 # 2
sdists(list(c(2,2,3),c(2,4,3)),weight=c(1,0,1)) # 1
### character data
w <- matrix(-1,nrow=8,ncol=8)                   # weight/score matrix for
diag(w) <- 0                                    # longest common subsequence
colnames(w) <- c("",letters[1:7])
x <- sapply(rbinom(3,64,0.5),function(n,x)
    paste(sample(x,n,rep=TRUE),collapse=""),
    colnames(w)[-1])
sdists(x,method="aw",weight=w)
diag(w) <- seq(0,7)
sdists(x,method="aw", weight=w)                 # global alignment
sdists(x,method="awl",weight=w)                 # local alignment
### missing values
sdists(list(c(2,2,3),c(2,NA,3)),exclude=NULL)   # 2 (inlcude anything)
sdists(list(c(2,2,3),c(2,NA,3)),exclude=NA)     # NA

[Package cba version 0.1-8 Index]