prepareAnnotations: prepare reference annotations for long read RNA-Seq analysis...

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

prepare reference annotations for long read RNA-Seq analysis with Bambu

Description

prepare reference annotations for long read RNA-Seq analysis with Bambu

Usage

prepareAnnotations(x)

Arguments

x	A path to gtf file or a TxDb object.

Details

This function creates a reference annotation object which is used for transcript discovery and quantification in Bambu. prepareAnnotations can use a path to a gtf file or a TxDB object as input, and returns a annotation object that stores additional information about transcripts which is used in Bambu. For each transcript, exons are ranked from first to last exon in direction of transcription.

Value

A GRangesList object with additional details for each exon and transcript that are required by Bambu. Exons are ranked by the exon_rank column, corresponding to the rank in direction of transcription (from first to last exon). In addition to exon rank, gene id, transcript id, and the minimum transcript equivalent class is stored as well (a transcript equivalence class of a transcript x is the collection of transcripts where their exon junctions contain, in a continuous way, the exon junctions of the transcript x). The object is designed to be used by Bambu, and the direct access of the metadata is not recommended.

See Also

[bambu()] for transcript discovery and quantification from long read RNA-Seq.

Examples

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

# run bambu
test.bam <- system.file("extdata", 
    "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam", 
    package = "bambu")
fa.file <- system.file("extdata", 
    "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa", 
    package = "bambu")
se <- bambu(reads = test.bam, annotations = annotations, 
    genome = fa.file, discovery = TRUE, quant = TRUE)

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