EXPANDS 1.7.1 release

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EXPANDS

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Mar 28, 2016, 10:23:22 AM3/28/16
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EXPANDS 1.7.1 is now available on CRAN:

 

https://cran.r-project.org/web/packages/expands

 

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CHANGES IN EXPANDS VERSION 1.7.1

 

o Higher subpopulation detection specificity, in particular for small subpopulations. The incidence at which heterozygous and homozygous state of a single subpopulation are falsesly confounded as two distinct subpopulations is reduced.

 

NEW FEATURES

 

o 50 simulated samples of various genetic complexities and noise levels included for user testing.

o Whenever possible, SNVs are assigned not only to the subpopulation in which they first occurred, but also to descending subpopulations.

o New phylogeny plotting option: user can choose between consensus and germline population to be included as control.

o New subpopulation plotting options (function plotSPs).

o Two additional output files are created: subpopulation specific ploidy matrix and a summary file of all detected subpopulations, including information on the inferred ancestor and the closest descendant of each subpopulation.

 

BUG FIXES

 

o Fixed bug where rare scenarios would lead to wrong subpopulation specific ploidy assignments at specific mutated loci.

 

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