optimizedTranscriptLengths {ORFik} | R Documentation

## Load length of all transcripts

### Description

A speedup wrapper around `transcriptLengths`, default load time of lengths is ~ 15 seconds, if ORFik fst optimized lengths object has been made, load that file instead: load time reduced to ~ 0.1 second.

### Usage

    optimizedTranscriptLengths(
      txdb,
      with.utr5_len = TRUE,
      with.utr3_len = TRUE,
      create.fst.version = FALSE
    )

### Arguments

`txdb` | a TxDb file or a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite), if it is a GRangesList, it will return it self.
`with.utr5_len` | logical TRUE, include length of 5' UTRs, ignored if .fst exists
`with.utr3_len` | logical TRUE, include length of 3' UTRs, ignored if .fst exists
`create.fst.version` | logical, FALSE. If TRUE, creates a .fst version of the transcript length table (if it not already exists), reducing load time from ~ 15 seconds to ~ 0.01 second next time you run filterTranscripts with this txdb object. The file is stored in the same folder as the genome this txdb is created from, with the name: `paste0(ORFik:::remove.file_ext(metadata(txdb)[3,2]), "_", gsub(" \(.*| |:", "", metadata(txdb)[metadata(txdb)[,1] == "Creation time",2]), "_txLengths.fst")` Some error checks are done to see this is a valid location, if the txdb data source is a repository like UCSC and not a local folder, it will not be made.

### Value

a data.table of loaded lengths 8 columns, 1 row per transcript isoform.

[Package ORFik version 1.14.7 Index]