Re^3: Pair-Wise Clustering

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Re^4: Pair-Wise Clustering by cutcopy11 (Initiate) on Oct 01, 2009 at 03:58 UTC
Yes, I believe that is the correct data structure. I have used this data structure to count occurrences of dna motifs at various positions. Say, I wanted to count and store the total occurences of A, C, G, T in 1000 nucleotide sequences that are 10 nucleotides long at each position. If you wanted a hash of arrays with the keys being A,C,G,T and the elements being positions 1 through 10, then `$position[10]{A}` [download] would equal the frequency of A at position 10 if you define position 1 as element 1. ... anyway, yes, this is the data structure that I want to store the clusters in, but I still need to figure out how to write a code to determine those clusters. I am still working on it. I think that I might have figured it out, though it is quite crude.	[reply] [d/l]

Replies are listed 'Best First'.

Re^4: Pair-Wise Clustering
by cutcopy11 (Initiate) on Oct 01, 2009 at 03:58 UTC

Yes, I believe that is the correct data structure. I have used this data structure to count occurrences of dna motifs at various positions. Say, I wanted to count and store the total occurences of A, C, G, T in 1000 nucleotide sequences that are 10 nucleotides long at each position. If you wanted a hash of arrays with the keys being A,C,G,T and the elements being positions 1 through 10, then

$position[10]{A}
[download]

would equal the frequency of A at position 10 if you define position 1 as element 1. ... anyway, yes, this is the data structure that I want to store the clusters in, but I still need to figure out how to write a code to determine those clusters. I am still working on it. I think that I might have figured it out, though it is quite crude.

[reply]
[d/l]