library(Biostrings) S_seq = "acgtggattagcgta"; Q_seq = "acgtcgta"; xq = DNAString(Q_seq); xs = DNAString(S_seq);
m = length(xq); n = length(xs); score_matrix = matrix(data=0, nrow = m+1, ncol = n+1, byrow = TRUE) best=0; optloc=c(0,0); for (i in 2:(m+1)){ for (j in 2:(n+1)){ if ((xs[i-1]) == (xq[j-1])) {score.match = 3} else {score.match = -4} score_matrix[i,j]=max(score_matrix[i,j-1]-7, score_matrix[i-1,j]-7, score_matrix[i-1,j-1] + score.match); if (score_matrix[i,j]>= best) { best = score_matrix[i,j]; optloc = c(i,j); } } } Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains NAs or out-of-bounds indices Can somebody help me with this error. What does it mean? I updated all the packages I used and I'm a newbie to this so I would really appreciate some help. Here is my sessionInfo:R version 3.1.3 (2015-03-09) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] Biostrings_2.34.1 XVector_0.6.0 IRanges_2.0.1 S4Vectors_0.4.0 [5] BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] tools_3.1.3 zlibbioc_1.10.0 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel