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evogytis / fluB

Investigating the (co)evolution of reassorting influenza B lineages.
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LD improvement. #23

Closed evogytis closed 10 years ago

evogytis commented 10 years ago

The analysis of linkage disequilibrium (p.10/11) can be improved. The discussion contains some misleading statements; for example, linkage disequilibrium does not depend only single-site allele frequencies, but also on the pair frequencies. More importantly, it is better to use a normalized measure such as D' (Lewontin 1964), which is not confounded by differences in nucleotide diversity between segments and between individual sites within segments. This possible confounding factor may affect the inference of a co-assorting site network in Fig.S7.

evogytis commented 10 years ago

Ready to address this with the streamlined LD calculator (83baed37bdb77f1a7d55d069f06ecaa273eb2cb7) on the most recent download of Genbank's influenza B sequence data which has about 1600 complete genomes.