pm_binom: Binomial mixture fitting

In ampatzia/pasaR: Pangenome Statistical Analysis for R

Description

This function determines the closedness of the pangenome using a binomial mixture fit of the data.

Usage

pm_binom(Panmatrix, K.range = 2:8, core.detect.prob = 1)

Arguments

Panmatrix	Panmatrix produced by make_panmatrix functions
K.range	Range of model components to be tested, defaults to search from 2 to 8
core.detect.prob	Detection probability of core genes. Defaults to 1.0

Details

The function returns pangenome and core size estimation along with the propabilities of the components.This is an optimized version of the binomixEstimate() function from package micropan (Snipen & Hiland, 2015).

References

L. Snipen and K. H. Liland, "micropan: an R-package for microbial pan-genomics.," BMC bioinformatics, vol. 16, p. 79, 2015

Examples

## Not run: pm_binom(panm, K.range =2:8)

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