Description Usage Arguments Details References Examples
This function determines the closedness of the pangenome using a curve fit of the data based on Heaps Law.
1 | pm_heaps(Panmatrix, n_perm)
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Panmatrix |
Panmatrix produced by make_panmatrix functions |
n_perm |
Number of permutations |
The regression fit returns two estimated parameters, intercept and decay parameter a. If a<1 then the pangenome is considered to be open. This is an optimized version of the heaps() function from package micropan. The theoretical aspects are discussed in the canonical work of Tettelin et al. (2008)
Tettelin, H., Riley, D., Cattuto, C., Medini, D. (2008). Comparative genomics: the bacterial pan-genome. Current Opinions in Microbiology, 12:472-477.
1 | ## Not run: pm_heaps(Panmatrix,n_perm=100)
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