[Bioc-devel] Biostring

a_kinga at yahoo.com a_kinga at yahoo.com
Sun Apr 26 13:52:45 CEST 2015

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)

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-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)

[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

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