nc.adj {tAI} | R 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).
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")
[Package tAI version 0.2.2 Index]