organism,experiment-method {ORFik} | R Documentation

## Get ORFik experiment organism

### Description

If not defined directly, checks the txdb / gtf organism information, if existing.

### Usage

    ## S4 method for signature 'experiment'
    organism(object)

### Arguments

`object` | an ORFik `experiment`

### Value

character, name of organism

### 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)

    #' 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(read.experiment("new-experiment))

[Package ORFik version 1.12.13 Index]