The pairwiseAlignment() function have a problematic way of handling empty sequences illustrated by this toy example:

library(Biostrings)

seq1 <- DNAString('ATCG')
seq2 <- DNAString('')
 
tmp <- pairwiseAlignment(seq1, seq2)
class(tmp)
[1] "PairwiseAlignmentsSingleSubject"
attr(,"package")
[1] "Biostrings"

tmp
Global PairwiseAlignmentsSingleSubject (1 of 1)
Error in rep(" ", patternSpaces) : invalid 'times' argument
In addition: Warning message:
In function (object)  : NaNs produced

My inituition would be that pairwiseAlignment it simply repported no overlap and a score of NA.

Btw this error crashes RStudio-

Hi Kristoffer,

Sorry that it took so long but this was a low-priority issue. It should be fixed in Biostrings 2.47.3:

library(Biostrings)
pattern <- DNAString("ATCG")
subject <- DNAString("")
pairwiseAlignment(pattern, subject)
# Global PairwiseAlignmentsSingleSubject (1 of 1)
# pattern: [1] ""
# subject: [1] ""
# score: -26 

The score of -26 reflects the cost of the gap introduced by the full deletion required to globally align "ATCG" to "". Given that the default values of gapOpening and gapExtension are 10 and 4, respectively, the cost of this gap is gapOpening + 4 * gapExtension = 26.

Biostrings 2.47.3 should become available via biocLite() to Bioconductor devel users in the next 48 hours or so.

Cheers,

H.