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everhartlab / sclerotinia-366

Analysis for "Population structure and phenotypic variation of *Sclerotinia sclerotiorum* from dry bean (*Phaseolus vulgaris*) in the United States"
https://doi.org/10.7717/peerj.4152
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Investigate statistical measures for mlg/mcg graph #7

Closed zkamvar closed 7 years ago

zkamvar commented 7 years ago

The MLG-MCG graph is also known as a bipartite network. This is a special kind of network where there are two kinds of nodes and connections may only be between nodes of different types.

A simple method to test this would be to compare it with random graphs using igraph's sample_bipartite(), but there are several papers that talk about statistical inference of these graphs:

Strona and Veech, 2015 (Methods in Ecology and Evolution) Saracco et al., 2015 (Scientific Reports) Yildrim and Cosica, 2014 (PLoS One)

I have not yet read these papers deeply, but given the size of our data set, we have a good chance of more formally investigating this angle.

zkamvar commented 7 years ago

Modularity gives us an assessment of how connected things are.