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[Bioc-devel] Biostring

2 messages · a_kinga at yahoo.com, Martin Morgan

Original
a_kinga at yahoo.com
# 
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
Martin Morgan
#
On 04/26/2015 04:52 AM, Kinga via Bioc-devel wrote:
for j = 10, xq[j - 1] tries to access the 9th letter of Q_seq. But Q_seq only 
has 8 letters. Did you mean

     xs[j-1] == xq[i-1]

?

This question probably belongs on https://support.bioconductor.org

Martin