# Translational Efficiency Regulation Analysis using the PADOG Method

## Documentation for package ‘terapadog’ version 1.3.0

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

## Help Pages

get_FCs | This function execute the Differential Translation Analysis on its own using DeltaTE. The output is a dataframe with the FC in mRNA counts, RIBO counts or TE between the conditions in exam.
id_converter | Convert the human gene identifier (hgnc_symbol or ensembl_gene_id) to entrezgene_id format for the analysis.
plotDTA | This function will plot an interactive html plot of the results of get_FCs.R That is to say, a plot of the genes undergoing translational regulation, coloured by RegMode. Genes whose RegMode was Undeterminable or Undetermined are omitted.
prepareTerapadogData | Prepare Data by Loading and Validating RNA, RIBO Counts, and Metadata. This function reads RNA and RIBO count files, checks input data validity and merges them into a single numerical matrix (expression.data). It also prepares the metatadata needed by padog (exp_de).
terapadog | Performs the main Gene Set Enrichement Analysis, by applying a modified version of the PADOG algorithm to genes undergoing changes in TE.