pm_fluidity: Genome Fluidity with sampling

In ampatzia/pasaR: Pangenome Statistical Analysis for R

Description

This function computes fluidity with sampling, as implemented on package micropan (optimized for speed). Fluidity takes values in [0,1], with 1 denoting no common genes.

Usage

pm_fluidity(Panmatrix, n.sim = 10)

Arguments

Panmatrix	Panmatrix produced by make_panmatrix functions
n.sim	Number of simulations,defaults to 10

Details

Fluidity takes values in [0,1], with 1 denoting no common genes.This metric was introduced is called the Sorensen distance (Deza & Deza, 2009) and was first introduced in the context of a pangenome analysis in (Kislyuk et al ,2011).

References

A. O. Kislyuk, B. Haegeman, N. H. Bergman, and J. S. Weitz, "Genomic fluidity???: an integrative view of gene diversity within microbial populations," BMC genomics, pp. 12-32, 2011. M. M. Deza and E. Deza, Encyclopedia of Distances. Springer, 2009.

Examples

## Not run: pm_fluidity(Panmatrix, n.sim=100)

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