heaps: Heaps law estimate
In micropan: Microbial Pan-Genome Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

Estimating if a pan-genome is open or closed based on a Heaps law model.

1	heaps(pan.matrix, n.perm = 100)

`pan.matrix`	A pan-matrix, see `panMatrix` for details.
`n.perm`	The number of random permutations of genome ordering.

An open pan-genome means there will always be new gene clusters observed as long as new genomes are being sequenced. This may sound controversial, but in a pragmatic view, an open pan-genome indicates that the number of new gene clusters to be observed in future genomes is ‘large’ (but not literally infinite). Opposite, a closed pan-genome indicates we are approaching the end of new gene clusters.

This function is based on a Heaps law approach suggested by Tettelin et al (2008). The Heaps law model is fitted to the number of new gene clusters observed when genomes are ordered in a random way. The model has two parameters, an intercept and a decay parameter called alpha. If alpha>1.0 the pan-genome is closed, if alpha<1.0 it is open.

The number of permutations, n.perm, should be as large as possible, limited by computation time. The default value of 100 is certainly a minimum.

Word of caution: The Heaps law assumes independent sampling. If some of the genomes in the data set form distinct sub-groups in the population, this may affect the results of this analysis severely.

A vector of two estimated parameters: The Intercept and the decay parameter alpha. If alpha<1.0 the pan-genome is open, if alpha>1.0 it is closed.

Lars Snipen and Kristian Hovde Liland.

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

binomixEstimate, chao, rarefaction.

# Loading a pan-matrix in this package 
data(xmpl.panmat)

# Estimating population openness
h.est <- heaps(xmpl.panmat, n.perm = 500)
print(h.est)
# If alpha < 1 it indicates an open pan-genome