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
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