The package can calculate the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp's method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) Translational accuracy selection can be inferred from Akashi's test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons biased used in the highly expressed genes), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi's test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function proportion_index in the package. The function focus on the proportion of optimal codon against its corresponding non-optimal codons for the the four and six codon boxes.

Install the latest version of this package by entering the following in R:

```
source("https://bioconductor.org/biocLite.R")
biocLite("sscu")
```

Author | Yu Sun |

Bioconductor views | GeneExpression Genetics WholeGenome |

Date of publication | None |

Maintainer | Yu Sun <sunyu1357@gmail.com> |

License | GPL (>= 2) |

Version | 2.2.0 |

**akashi_test:** akashi test for codon usage

**genomic_gc3:** genomic gc3 for an multifasta genomic file

**op_corre_CodonW:** Identify optimal codons by using the correlative method from...

**op_corre_NCprime:** Identify optimal codons by using the correlative method from...

**op_highly:** Identify optimal codons by using the highly expressed genes...

**optimal_codon_statistics:** statistical table for the optimal codons

**proportion_index:** optimal codons index for the four and six codon boxes

**s_index:** S index (Strength of Selected Codon Usage)

**sscu-package:** Strength of Selected Codon Usage

DESCRIPTION

NAMESPACE

NEWS

R

R/akashi_test.R
R/genomic_gc3.R
R/op_corre_CodonW.R
R/op_corre_NCprime.R
R/op_highly.R
R/optimal_codon_statistics.R
R/proportion_index.R
R/s_index.R
build

build/partial.rdb

inst

inst/akashi_test

inst/akashi_test/bifidos_alignments

inst/akashi_test/bifidos_alignments/0001.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0002.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0003.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0004.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0005.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0006.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0007.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0008.fas.ffn.mafft

inst/akashi_test/bifidos_alignments/0009.fas.ffn.mafft

inst/akashi_test/contingency_file_Gvag

inst/akashi_test/make_contingency_table.pl

inst/correlative_test

inst/correlative_test/Gvag.codonw

inst/correlative_test/LbDelBA1.NCprime

inst/sequences

inst/sequences/Gvag_genome_cds.ffn

inst/sequences/Gvag_highly.ffn

inst/sequences/L_kunkeei_genome_cds.ffn

inst/sequences/L_kunkeei_highly.ffn

inst/sequences/LbDelBA1_genome_cds.ffn

man

man/akashi_test.Rd
man/genomic_gc3.Rd
man/op_corre_CodonW.Rd
man/op_corre_NCprime.Rd
man/op_highly.Rd
man/optimal_codon_statistics.Rd
man/proportion_index.Rd
man/s_index.Rd
man/sscu-package.Rd
vignettes

vignettes/sscu.Rmd

vignettes/sscu.html

vignettes/sscu.pdf

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

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