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FIX: method.rst: Change Wikipedia to paper links
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thiago-miller committed Dec 25, 2019
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The denser (covered) the region the greater the chance of a
retrotransposition event there.

For more informations about the algorithm, a good start point
is the Wikipedia article: https://en.wikipedia.org/wiki/DBSCAN.

Genotype
========

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Spearman's rank correlation coefficient
---------------------------------------

We use Spearman's rank correlation coefficient (see Wikipedia article:
https://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient) in
order to have a **measure** of relationship between *reads* from exon and their
mates from clustering site. As our data is **nonparametric**, the Spearman's rho
can assess **monotonic** relationship, that is, it can tell us if the genomic
position of *reads* from exon **increases** when **does** the genomic position of
their *mates* from clustering site (positive rho) - or the opposite (negative rho).
We use *Spearman's rank correlation coefficient* [4]_ in order to have a
**measure** of relationship between *reads* from exon and their mates from
clustering site. As our data is **nonparametric**, the Spearman's rho can
assess **monotonic** relationship, that is, it can tell us if the genomic
position of *reads* from exon **increases** when **does** the genomic
position of their *mates* from clustering site (positive rho) - or the
opposite (negative rho).

So we come to the following proposition:

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A statistical framework for SNP calling, mutation discovery, association mapping and
population genetical parameter estimation from sequencing data.
Oxford University Press.
.. [4] Fieller, E. C., et al. (1957).
Tests for Rank Correlation Coefficients. I.
Biometrika, 44(3/4), 470–481. JSTOR.
Available at https://www.jstor.org/stable/2332878.

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