## ----file_settings, include = FALSE-------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.width = 6,
    fig.height = 4,
    dpi = 96,
    dev = "png"
)

## ----setup, message = FALSE, warning = FALSE, eval = FALSE--------------------
# if (!requireNamespace("BiocManager", quietly = TRUE)) {
#     install.packages("BiocManager")
# }
# 
# BiocManager::install("tTEscanR")

## ----load_setup, message = FALSE, warning = FALSE-----------------------------
library(tTEscanR)

## ----load_biomart, message = FALSE, warning = FALSE---------------------------
library(biomaRt)

## ----datasets_ensembl, message = TRUE, warning = FALSE, eval = FALSE----------
# datasets <- biomaRt::listDatasets(useEnsembl(biomart = "ensembl"))

## ----canonical_codon_freq, message = TRUE, warning = FALSE, eval = FALSE------
# codon_freq_results_canonical <- getCodonFreq(
#     dataset_name = "hsapiens_gene_ensembl", filter = "canonical",
#     retain_geneversion = TRUE,
#     retain_mitochondrial = FALSE, out_format = "external_gene_name"
# )

## ----canonical_results, message = TRUE, warning = FALSE, eval = FALSE---------
# hg38_codon_freq_table_canonical <- codon_freq_results_canonical[[2]]
# hg38_gene_translator_table_canonical <- codon_freq_results_canonical[[1]]

## ----length_codon_freq, message = TRUE, warning = FALSE, eval = FALSE---------
# codon_freq_results_length <- getCodonFreq(
#     dataset_name = "mmusculus_gene_ensembl", filter = "length",
#     retain_mitochondrial = TRUE, out_format = "ensembl_gene_id"
# )

## ----length_results, message = TRUE, warning = FALSE, eval = FALSE------------
# mm39_codon_freq_table_length <- codon_freq_results_length[[2]]
# mm39_gene_translator_table_length <- codon_freq_results_length[[1]]

## ----transcript_codon_freq, message = TRUE, warning = FALSE, eval = FALSE-----
# codon_freq_results_transcript <- getCodonFreq(
#     dataset_name = "drerio_gene_ensembl", filter = "length",
#     retain_mitochondrial = TRUE, out_format = "ensembl_transcript_id"
# )

## ----transcript_results, message = TRUE, warning = FALSE, eval = FALSE--------
# drerio_codon_freq_table_length <- codon_freq_results_transcript[[2]]
# drerio_gene_translator_table_length <- codon_freq_results_transcript[[1]]

## ----session-info, echo=FALSE-------------------------------------------------
sessionInfo()