makeTxdbFromGenome {ORFik} | R Documentation

## Make txdb from genome

### Description

Make a Txdb with defined seqlevels and seqlevelsstyle from the fasta genome. This makes it more fail safe than standard Txdb creation. Example is that you can not create a coverage window outside the chromosome boundary, this is only possible if you have set the seqlengths.

### Usage

    makeTxdbFromGenome(gtf, genome = NULL, organism, optimize = FALSE)

### Arguments

`gtf` | path to gtf file
`genome` | character, default NULL. Path to fasta genome corresponding to the gtf. If NULL, can not set seqlevels. If value is NULL or FALSE, it will be ignored.
`organism` | Scientific name of organism, first letter must be capital! Example: Homo sapiens. Will force first letter to capital and convert any "_" (underscore) to " " (space)
`optimize` | logical, default FALSE. Create a folder within the folder of the gtf, that includes optimized objects to speed up loading of annotation regions from up to 15 seconds on human genome down to 0.1 second. ORFik will then load these optimized objects instead. Currently optimizes filterTranscript() function and loadRegion() function for 5' UTRs, 3' UTRs, CDS, mRNA (all transcript with CDS) and tx (all transcripts).

### Value

NULL, Txdb saved to disc named paste0(gtf, ".db")

### Examples

    gtf <- "/path/to/local/annotation.gtf"
    genome <- "/path/to/local/genome.fasta"
    #makeTxdbFromGenome(gtf, genome, organism = "Saccharomyces cerevisiae")

[Package ORFik version 1.12.13 Index]