readFromGTF: convert a GTF file into a GRangesList

In GoekeLab/bambu: Context-Aware Transcript Quantification from Long Read RNA-Seq data

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)

GoekeLab/bambu documentation built on Oct. 26, 2024, 9:45 a.m.