levenAlign | R Documentation |
Align strings to a reference string based on Levenshtein distance with ends-free or homopolymer alignments possible
levenAlign(
strings,
ref,
homoLimit = 0,
prepend = NULL,
append = NULL,
substring1 = FALSE,
substring2 = FALSE,
trimOuterGaps = FALSE,
revComp = FALSE,
...
)
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 |
A list with first entry for the gapped reference and second entry all the aligned strings
Scott Sherrill-Mix R@sherrillmix.com
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