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

Source: R/readWrite.R

Outputs a GTF file, transcript-count file, and gene-count file from bambu

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

Value

The function will generate three files, a .gtf file for the annotations, two .txt files for transcript and gene counts respectively.

Examples

se <- readRDS(system.file("extdata",
    "seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds",
    package = "bambu"
))
path <- tempdir()
writeBambuOutput(se, path)
#> Error in `:=`(TXNAME, "Incomaptible"): Check that is.data.table(DT) == TRUE. Otherwise, := and `:=`(...) are defined for use in j, once only and in particular ways. See help(":=").