organism.df: Get organism of the ORFik experiment

In ORFik: Open Reading Frames in Genomics

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))

ORFik documentation built on March 27, 2021, 6 p.m.