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.zf(), 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))

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