organism.df {ORFik} | R Documentation

## Get organism of the ORFik experiment

### Description

Uses the txdb / gtf organism information, if existing.

### Usage

    organism.df(df)

### Arguments

`df` | an ORFik `experiment`

### Value

organism (character vector), if no organism set: NA

### See Also

Other ORFik_experiment: `ORFik.template.experiment()`, `bamVarName()`, `create.experiment()`, `experiment-class`, `filepath()`, `libraryTypes()`, `outputLibs()`, `read.experiment()`, `save.experiment()`, `validateExperiments()`

### Examples

    # if you have set organism in txdb of
    # ORFik experiment:
    df <- ORFik.template.experiment()
    #organism.df(df)

    #' If you have not set the organism you can do:
    #txdb <- GenomicFeatures::makeTxDbFromGFF("pat/to/gff_or_gff")
    #BiocGenerics::organism(txdb) <- "Homo sapiens"
    #saveDb(txdb, paste0("pat/to/gff_or_gff", ".db"))
    # then use this txdb in you ORFik experiment and load:
    # create.experiment(exper = "new_experiment",
    #   txdb = paste0("pat/to/gff_or_gff", ".db")) ...
    # organism.df(read.experiment("new-experiment))

[Package ORFik version 1.10.13 Index]