organism-experiment-method: Get ORFik experiment organism

In JokingHero/ORFik: Open Reading Frames in Genomics

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(), ORFik.template.experiment.zf(), 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:
#gtf <- "pat/to/gff_or_gff"
#txdb_path <- paste0(gtf, ".db") # This file is created in next step
#txdb <- makeTxdbFromGenome(gtf, genome, organism = "Homo sapiens",
# optimize = TRUE, return = TRUE)
# then use this txdb in you ORFik experiment and load:
# create.experiment(exper = "new_experiment",
#   txdb = txdb_path) ...
# organism(read.experiment("new-experiment))

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.