dia.bactgensize {seqinr}R Documentation

Distribution of bacterial genome size from GOLD

Description

This function tries to download the last update of the GOLD (Genomes OnLine Database) to extract bacterial genomes sizes when available. The histogram and the default density() output is produced. Optionally, a maximum likelihood estimate of a superposition of two or three normal distributions is also represented

Usage

dia.bactgensize(fit = 2, p = 0.5, m1 = 2000, sd1 = 600, m2 = 4500,
       sd2 = 1000, p3 = 0.05, m3 = 9000, sd3 = 1000)

Arguments

fit integer value. If fit == O no normal fit is produced, if fit == 2 try to fit a superposition of two normal distributions, if fit == 3 try to fit a superposition of three normal distribution.
p initial guess for the proportion of the first population.
m1 initial guess for the mean of the first population.
sd1 initial guess for the standard deviation of the first population.
m2 initial guess for the mean of the second population.
sd2 initial guess for the standard deviation of the second population.
p3 initial guess for the proportion of the third population.
m3 initial guess for the mean of the third population.
sd3 initial guess for the standard deviation of the second population.

Value

An invisible dataframe with three components:

comp1 genus name
comp2 species names
comp3 genome size in Kb

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

density

Examples

  ## Not run: dia.bactgensize()

[Package seqinr version 1.0-4 Index]