writeBambuOutput: Write Bambu results to GTF and transcript/gene-count files

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

Write Bambu results to GTF and transcript/gene-count files

Description

Write Bambu results to GTF and transcript/gene-count files

Usage

writeBambuOutput(se, path, prefix = "")

Arguments

se	a SummarizedExperiment object from bambu.
path	the destination of the output files (gtf, transcript counts, and gene counts)
prefix	the prefix of the output files

Details

The function will write the output from Bambu to files. The annotations will be written to a .gtf file, transcript counts (total counts, CPM, full-length counts, partial-length counts, and unique counts) and gene counts will be written to .txt files.

Examples

se <- readRDS(system.file("extdata",
    "seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
    package = "bambu"
))
path <- tempdir()
writeBambuOutput(se, path)

GoekeLab/bambu documentation built on April 6, 2024, 10:36 p.m.