search for: substitutionmatrix

...to be IRanges ? Sometimes it's IntegerList, sometimes it's IRanges. For example, > A 11-letter "DNAString" instance seq: GAACGAGGACC > B 8-letter "DNAString" instance seq: GGACGAGC > alignment <- pairwiseAlignment(A, B, gapOpening = 0, gapExtension = 1, substitutionMatrix = substitutions) > alignment at subject@mismatch IntegerList of length 1 [[1]] 2 > alignment at subject@indel IRangesList of length 1 [[1]] IRanges of length 1 start end width [1] 8 9 2 Lastly, why are functions like insertion, deletion, and indel documented in Numeric Summary...