levenAlign: Align many strings to a reference

Description Usage Arguments Value Author(s) References

View source: R/leven.R

Description

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

Usage

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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 [email protected]

References

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


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