The Chao lower bound estimate of pan-genome size
Computes the Chao lower bound estimated number of gene clusters in a pan-genome.
chao(pan.matrix)
pan.matrix |
A pan-matrix, see |
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 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 this.
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.
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.
Lars Snipen and Kristian Hovde Liland.
Chao, A. (1987). Estimating the population size for capture-recapture data with unequal catchability. Biometrics, 43:783-791.
# Loading a pan-matrix in this package data(xmpl.panmat) # Estimating the pan-genome size using the Chao estimator chao.pansize <- chao(xmpl.panmat)
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