cubfits (version 0.1-2)

SCUO Index: Function for Synonymous Codon Usage Order (SCUO) Index

Description

Calculate the Synonymous Codon Usage Order (SCUO) index for each gene. Used as a substitute for expression in cases of without expression measurements.

Usage

calc_scuo_values(codon.counts)

Arguments

codon.counts

an object of format scuo.

Value

SCUO indices are returned.

Details

This function computes SCUO index for each gene. Typically, this method is completely based on entropy and information theory to estimate expression values of sequences according to their codon information.

References

http://www.tandfonline.com/doi/abs/10.1080/03081070500502967

Wan X.-F., Zhou J., Xu D. ``CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes'' International Journal of General Systems Vol. 35, Iss. 1, 2006.

See Also

scuo.random(), calc_cai_values(), calc_scu_values().

Examples

## Not run: 
# suppressMessages(library(cubfits, quietly = TRUE))
# 
# y.scuo <- convert.y.to.scuo(ex.train$y)
# SCUO <- calc_scuo_values(y.scuo)$SCUO
# plotprxy(ex.train$phi.Obs, SCUO, ylab = "SCUO (log10)")
# ## End(Not run)