readFromGTF: convert a GTF file into a GRangesList

In bambu: Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Description

Outputs GRangesList object from reading a GTF file

Usage

readFromGTF(file)

Arguments

file	a .gtf file

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)

bambu documentation built on Nov. 12, 2020, 2:01 a.m.