The Chao lower bound estimate of pan-genome size

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Description

Computes the Chao lower bound estimated number of gene clusters in a pan-genome.

Usage

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chao(pan.matrix)

Arguments

pan.matrix

A Panmat object, see panMatrix for details.

Details

The size of a pan-genome is the number of gene clusters in it, both those observed and those not yet observed.

The input pan.matrix is a Panmat object, i.e. it is a matrix with one row for each genome and one column for each observed gene cluster in the pan-genome. See panMatrix for how to construct such objects.

The number of observed gene clusters is simply the number of columns in pan.matrix. The number of gene clusters not yet observed is estimated by the Chao lower bound estimator (Chao, 1987). This is based solely on the number of clusters observed in 1 and 2 genomes. It is a very simple and conservative estimator, i.e. it is more likely to be too small than too large.

Value

The function returns an integer, the estimated pan-genome size. This includes both the number of gene clusters observed so far, as well as the estimated number not yet seen.

Author(s)

Lars Snipen and Kristian Hovde Liland.

References

Chao, A. (1987). Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43:783-791.

See Also

panMatrix, binomixEstimate.

Examples

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# Loading a Panmat object in the micropan package
data(list="Mpneumoniae.blast.panmat",package="micropan")

# Estimating the pan-genome size using the Chao estimator
chao.pansize <- chao(Mpneumoniae.blast.panmat)

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