makeSymbols: Make Gene symbols from txdb
In Roleren/ORFik: Open Reading Frames in Genomics

makeSymbols

R Documentation

Make Gene symbols from txdb

Description

Make Gene symbols from txdb

Usage

makeSymbols(
  txdb,
  symbols_file_out_path = file.path(dirname(getGtfPathFromTxdb(txdb, stop.error = TRUE)),
    "gene_symbol_tx_table.fst"),
  uniprot_id = FALSE
)

Arguments

`txdb`	a TxDb file, a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite) or an ORFik experiment
`symbols_file_out_path`	path to save, default `file.path(dirname(getGtfPathFromTxdb(txdb, stop.error = TRUE)), "gene_symbol_tx_table.fst")`
`uniprot_id`	logical default FALSE. If TRUE, will download and store all uniprot id for all transcripts (coding and noncoding)- In a file called: "gene_symbol_tx_table.fst" in same folder as txdb.