optimize: Optimal Coverage and Identity Thresholds
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Value Author(s) See Also

For a given locus, get threshold values for minimum coverage and minimum identity that allow to include at least one sequence of every species in the database.

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optimizeCoverage(x, discard = 0, quiet = FALSE, plot = FALSE)

optimizeIdentity(x, discard = 0, quiet = FALSE, plot = FALSE)

`x`	an object of class `megapteraProj`.
`discard`	integer, giving the number of species to ‘sacrifice’; e.g. if `discard = 2`, the threshold value is chosen such that all but two species will be selected for the final alignment.
`quiet`	logical, indicating if screen output should be suppressed.
`plot`	logical:

a list with three elements:

`current`	current threshold value
`suggested`	suggest threshold value to include all species
`ranking`	maximum identity/coverage values for each species in ascending order