pm_heaps: Heap's Law fitting

In ampatzia/pasaR: Pangenome Statistical Analysis for R

Description

This function determines the closedness of the pangenome using a curve fit of the data based on Heaps Law.

Usage

pm_heaps(Panmatrix, n_perm)

Arguments

Panmatrix	Panmatrix produced by make_panmatrix functions
n_perm	Number of permutations

Details

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)

References

Tettelin, H., Riley, D., Cattuto, C., Medini, D. (2008). Comparative genomics: the bacterial pan-genome. Current Opinions in Microbiology, 12:472-477.

Examples

 ## Not run: pm_heaps(Panmatrix,n_perm=100)

ampatzia/pasaR documentation built on May 12, 2019, 2:37 a.m.