levenAll: Wrapper for .C Levenshtein function

Description Usage Arguments Value Author(s) References

View source: R/leven.R

Description

Align and calculate distance betweeen two strings based on Levenshtein distance with ends-free or homopolymer alignments possible (probably not called directly)

Usage

1
2
levenAll(string1, string2, homoLimit = 0, prepend = NULL, append = NULL,
  revComp = FALSE, align = FALSE, nThreads = 1)

Arguments

string1

A single string or vector of strings

string2

Another single string or vector of strings

homoLimit

deletions or insertions in homopolymers > homoLimit cost 0

prepend

1 or 2 for ends-free on front of string 1 or 2

append

1 or 2 for ends-free on back of string 1 or 2

revComp

Should the reverse compliment of string1 also be tested and the best of identity or reverse compliment returned?

align

Should an alignment be calculated

nThreads

If threads >1, run nThreads threads in parallel

Value

Either a distance or if align==TRUE a list with distance and alignment

Author(s)

Scott Sherrill-Mix [email protected]

References

http://en.wikipedia.org/wiki/Levenshtein_distance


sherrillmix/levenR documentation built on May 26, 2017, 8:08 a.m.