SCUO Index {cubfits} | R Documentation |
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 |
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.
Value
SCUO
indices are returned.
Author(s)
Drew Schmidt.
References
https://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)
[Package cubfits version 0.1-4 Index]