How to interpret a pairwise distance matrices for X nr-SNPs sliding windows across the genome
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6.9 years ago
serpalma.v ▴ 70

Hi everyone,

I am new at bioinformatic concepts such as sliding window algorithm. I am currently reading a paper where this concepts appears. And states:

We generated 13-by-13 pairwise distance matrices for 25-SNP sliding windows across the genome.

This is shown in figure 1D in Chan et al 2012.

http://linkinghub.elsevier.com/retrieve/pii/S0960982212002680

My questions are:

  • Can this be minimized to a simpler expression for the non-bioinformatic?
  • How to interpret the pair-wise distance matrix?
  • What background should I learn to understand this?

Thanks

SNP sliding-window • 2.8k views
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Entering edit mode
6.9 years ago
vassialk ▴ 200

Distances are mathematical concepts used in clustering algorithms for classifying and stratifying sets based on some input values. They are common in information retrieval and practical bioinformatics. You can pick a book on library genesis or Amazon to read about. Expander, MeV, Mayday, Cytoscape documentation is also informative. Good paper on it here http://link.springer.com/chapter/10.1007%2F978-3-642-13800-3_10.

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