Translational Efficiency Regulation Analysis using the PADOG Method

Documentation for package ‘terapadog’ version 1.5.2

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.
get_gene_from_kegg_pathway	This function retrieves, for a given pathway id, the member genes GeneID (ensembl) and gene name. It then extracts their rows from the results produced by get_FC, to allow the manual inspection of the genes within a pathway of interest.
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.
plot_pathway_changes	This function plots, for a given pathway id, the member genes RNA, RIBO, and TE fold changes on the relative pathway (3 plots). Only significant genes are plotted. Plots are saved as .png files.
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.