nc.adj: Adjusted effective number of codons (Nc)

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nc.adjR Documentation

Adjusted effective number of codons (Nc)

Description

The adjusted Nc is f(gc3s) - Nc

Usage

nc.adj(nc, gc3)

Arguments

nc

a vector of length n with the effective number of codons for genes

gc3

a vector of length n with corresponding GC composition at third codon positions

Details

The adjusted Nc is calculated as described in dos Reis et al. (2004).

Author(s)

Mario dos Reis

References

dos Reis M., Savva R., and Wernisch L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32: 5036–44.

See Also

nc.f for the function used to calculate f(gc3s)

Examples


eco.ncadj <- nc.adj(ecolik12$w$Nc, ecolik12$w$GC3s)
plot(eco.ncadj ~ ecolik12$w$Nc, xlab="Nc", ylab="Nc adjusted")


mariodosreis/tai documentation built on June 9, 2022, 7:37 p.m.