levenAlign: Align many strings to a reference

In sherrillmix/levenR: Simple Levenshtein Alignment and Distance Calculation

Align many strings to a reference

Description

Align strings to a reference string based on Levenshtein distance with ends-free or homopolymer alignments possible

Usage

levenAlign(
  strings,
  ref,
  homoLimit = 0,
  prepend = NULL,
  append = NULL,
  substring1 = FALSE,
  substring2 = FALSE,
  trimOuterGaps = FALSE,
  revComp = FALSE,
  ...
)

Arguments

strings	The query strings to be aligned
ref	The reference to align to
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
substring1	ends-free for query strings
substring2	ends-free for reference
trimOuterGaps	Trim leading and trailing gaps
revComp	Find and return the best alignment of identity or reverse compliment of queries
...	Additional arguments for levenAll

Value

A list with first entry for the gapped reference and second entry all the aligned strings

Author(s)

Scott Sherrill-Mix [e-mail]

References

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

sherrillmix/levenR documentation built on Oct. 25, 2023, 11:42 a.m.