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

In mariodosreis/tai: The tRNA Adaptation Index

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).

Value

A vector of length n with adjusted Nc values

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 15, 2025, 1:21 a.m.