On 04/26/2015 04:52 AM, Kinga via Bioc-devel wrote:
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}
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
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
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
