# Codon Usage Analysis and Prediction of Gene Expressivity

## Documentation for package ‘coRdon’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

coRdon-package | coRdon: codon usage analysis in R
B | Calculate CU measures.
B-method | Calculate CU measures.
Bplot | Karlin B plot
Bplot-method | Karlin B plot
CAI | Calculate CU expressivity measures.
CAI-method | Calculate CU expressivity measures.
codonCounts | An S4 class 'codonTable'
codonCounts-method | An S4 class 'codonTable'
codonTable | An S4 class 'codonTable'
codonTable-class | An S4 class 'codonTable'
codonTable-method | An S4 class 'codonTable'
codonUsage | Calculate CU measures.
codonUsage-expressivity | Calculate CU expressivity measures.
contable | An S4 class 'crossTab'
contable-method | An S4 class 'crossTab'
coRdon | coRdon: codon usage analysis in R
crossTab | An S4 class 'crossTab'
crossTab-class | An S4 class 'crossTab'
crossTab-method | An S4 class 'crossTab'
E | Calculate CU expressivity measures.
E-method | Calculate CU expressivity measures.
ENC | Calculate CU measures.
ENC-method | Calculate CU measures.
ENCprime | Calculate CU measures.
ENCprime-method | Calculate CU measures.
enrichBarplot | Barplot of enriched and depleted annotations.
enrichBarplot-method | Barplot of enriched and depleted annotations.
enrichMAplot | MA plot of enriched annotations.
enrichMAplot-method | MA plot of enriched annotations.
enrichMatrix | Extract chosen enrichment values to a matrix.
enrichMatrix-method | Extract chosen enrichment values to a matrix.
enrichment | Enrichment analysis for codon usage (CU) data.
enrichment-method | Enrichment analysis for codon usage (CU) data.
Fop | Calculate CU expressivity measures.
Fop-method | Calculate CU expressivity measures.
GCB | Calculate CU expressivity measures.
GCB-method | Calculate CU expressivity measures.
genCode | An S4 class 'genCode'
genCode-class | An S4 class 'genCode'
genCode-method | An S4 class 'genCode'
getCOG | An S4 class 'codonTable'
getCOG-method | An S4 class 'codonTable'
getID | An S4 class 'codonTable'
getID-method | An S4 class 'codonTable'
getKO | An S4 class 'codonTable'
getKO-method | An S4 class 'codonTable'
getlen | An S4 class 'codonTable'
getlen-method | An S4 class 'codonTable'
getSeqAnnot | An S4 class 'crossTab'
getSeqAnnot-method | An S4 class 'crossTab'
getVariable | An S4 class 'crossTab'
getVariable-method | An S4 class 'crossTab'
HD59 | Codon usage in healthy human gut microbiome.
HD59_KO | Codon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see '?HD59'.
HD59_PATHWAYS | Codon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see '?HD59'.
intraBplot | Intra-samples Karlin B plot
intraBplot-method | Intra-samples Karlin B plot
LD94 | Codon usage in human gut microbiome in liver cirrhosis.
LD94_KO | Codon usage based KO enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.
LD94_PATHWAYS | Codon usage based KEGG Pathway enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.
length-codonTable | Length of 'codonTable' object.
length-crossTab | Length of 'crossTab' object.
length-method | Length of 'codonTable' object.
length-method | Length of 'crossTab' object.
MCB | Calculate CU measures.
MCB-method | Calculate CU measures.
MELP | Calculate CU expressivity measures.
MELP-method | Calculate CU expressivity measures.
MILC | Calculate CU measures.
MILC-method | Calculate CU measures.
readSet | Read set of sequences.
reduceCrossTab | Reduce 'crossTab'.
reduceCrossTab-method | Reduce 'crossTab'.
RPKOs | KEGG Orthology (KO) annotations for ribosomal genes.
SCUO | Calculate CU measures.
SCUO-method | Calculate CU measures.
setCOG | An S4 class 'codonTable'
setCOG-method | An S4 class 'codonTable'
setKO | An S4 class 'codonTable'
setKO-method | An S4 class 'codonTable'
show-codonTable | Display the object of 'codonTable' class.
show-crossTab | Display the object of 'crossTab' class.
show-method | Display the object of 'codonTable' class.
show-method | Display the object of 'crossTab' class.
subset.codonTable | Subset 'codonTable' object.