Closed gevro closed 2 years ago
This is clarified in Biostrings 2.65.4. The man page for compareStrings()
(?compareStrings
) now says:
pattern, subject: The strings to compare. Can be of type ‘character’,
‘XString’, ‘XStringSet’, ‘AlignedXStringSet’, or, in the case
of ‘pattern’, ‘PairwiseAlignments’.
If the first argument of ‘compareStrings()’ (‘pattern’) is a
‘PairwiseAlignments’ object, then the second argument
(‘subject’) must be missing. In this case ‘compareStrings(x)’
is equivalent to ‘compareStrings(pattern(x), subject(x))’.
Biostrings 2.65.4 should become available in BioC 3.16 (devel) in the next 24-48 hours via BiocManager::install()
.
Thank you
Hi, Documentation of compareStrings is missing an explanation for what it does with input of: pattern="PairwiseAlignments", subject="missing"
I believe the best place to document this would be: PairwiseAlignments-class {Biostrings}