readFromGTF {bambu} | R Documentation

## convert a GTF file into a GRangesList

### Description

Outputs GRangesList object from reading a GTF file

### Usage

    readFromGTF(file, keep.extra.columns = NULL)

### Arguments

`file` | a .gtf file
`keep.extra.columns` | a vector with names of columns to keep from the the attributes in the gtf file. For ensembl, this could be keep.extra.columns=c('gene_name','gene_biotype', 'transcript_biotype', 'transcript_name')

### Value

grlist a `GRangesList` object, with two columns

TXNAME

  specifying prefix for new gene Ids (genePrefix.number), defaults to empty

GENEID

  indicating whether filter to remove read classes which are a subset of known transcripts(), defaults to TRUE

### Examples

    gtf.file <- system.file("extdata",
        "Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf",
        package = "bambu"
    )
    readFromGTF(gtf.file)

[Package bambu version 2.0.6 Index]