Description Usage Arguments Details References Examples
This function determines the closedness of the pangenome using a binomial mixture fit of the data.
1 | pm_binom(Panmatrix, K.range = 2:8, core.detect.prob = 1)
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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 |
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).
L. Snipen and K. H. Liland, "micropan: an R-package for microbial pan-genomics.," BMC bioinformatics, vol. 16, p. 79, 2015
1 | ## Not run: pm_binom(panm, K.range =2:8)
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