tTEscanR Codon Frequency-per-Gene Matrix

Overview

In this document, we present all the functionalities that the codon frequency-per-gene module incorporates.

# install.packages("/avarassanchez/tTEscanR")
library(tTEscanR)

The reference codon frequency-per-gene matrix represents the codon distribution of each protein-coding gene in a reference genome.

The getCodonFreq() function computes the reference codon frequency-per-gene matrix. It retrieves the codon composition table for any organism supported by Ensembl. The function returns a list containing: (i) a codon frequency-per-gene-matrix, and (ii) a gene translator table mapping between Ensembl IDs and gene names. This output can be used directly in downstream codon usage analyses.

library(biomaRt)
datasets <- biomaRt::listDatasets(useEnsembl(biomart = "ensembl"))

One of the main advantages of the getCodonFreq() function is that it can be applied to any organism available at Ensembl. As a reference we can use hsapiens_gene_ensembl for hg38 human genome and mmusculus_gene_ensembl for mm39 mouse genome. Other organism names can be extracted using datasets$dataset.

In the example below, we will use both human and mouse reference dataset and the canonical and length filters to show the potential of the getCodonFreq() function.

Example 1:
  • Reference hg38 dataset
  • Canonical filter
  • Removing mitochondrial genes
  • External gene name as output 
    • codon_freq_results_canonical <- getCodonFreq(
    dataset_name = "hsapiens_gene_ensembl", filter = "canonical",
    retain_geneversion = TRUE,
    retain_mitochondrial = FALSE, out_format = "external_gene_name"
)
    hg38_codon_freq_table_canonical <- codon_freq_results_canonical[[2]]
hg38_gene_translator_table_canonical <- codon_freq_results_canonical[[1]]
    Example 2:
  • Reference mm39 dataset
  • Length filter
  • Keeping mitochondrial genes
  • Ensembl gene id as output 
    • codon_freq_results_length <- getCodonFreq(
    dataset_name = "mmusculus_gene_ensembl", filter = "length",
    retain_mitochondrial = TRUE, out_format = "ensembl_gene_id"
)
    mm39_codon_freq_table_length <- codon_freq_results_length[[2]]
mm39_gene_translator_table_length <- codon_freq_results_length[[1]]
    Example 3:
  • Using a
  • Canonical filter
  • Removing mitochondrial genes
  • Ensembl transcript id as output 
    • codon_freq_results_transcript <- getCodonFreq(
    dataset_name = "drerio_gene_ensembl", filter = "length",
    retain_mitochondrial = TRUE, out_format = "ensembl_transcript_id"
)
    drerio_codon_freq_table_length <- codon_freq_results_transcript[[2]]
drerio_gene_translator_table_length <- codon_freq_results_transcript[[1]]
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