append_gene_symbols: Append gene symbols to a data.table with tx ids

In JokingHero/ORFik: Open Reading Frames in Genomics

Append gene symbols to a data.table with tx ids

Description

Main use case is to add gene symbols to data.table outputs from ORFik with tx ids only, like the DTEG.analysis etc.

Usage

append_gene_symbols(dt, symbols_dt, extend_id = TRUE, id_col = "id")

Arguments

dt	a data.table, must have a id_col with transcript ids
symbols_dt	the data.table with symbols, must have a column with tx, transcript or value in the name. And only 1 of those!
extend_id	logical, if TRUE, paste together old id from dt, with the symbol id like: tx_id(symbol_id)
id_col	character, default "id". The name of the id column in dt.

Value

a data.table

Examples

library(data.table)
df <- ORFik.template.experiment()

cds_names <- names(loadRegion(df, "cds"))
dt <- data.table(id = cds_names[-1], LFC = seq(5), p.value = 0.05)

symbols_dt <- data.table(ensembl_tx_name = cds_names,
 ensembl_gene_id = txNamesToGeneNames(cds_names, df),
 external_gene_name = c("ATF4", "AAT1", "ML4", "AST2", "RPL4", "RPL12"))
append_gene_symbols(dt, symbols_dt)
append_gene_symbols(dt, symbols_dt, extend_id = FALSE)

JokingHero/ORFik documentation built on June 9, 2025, 8:46 p.m.