organism,experiment-method {ORFik} | R Documentation |
If not defined directly, checks the txdb / gtf organism information, if existing.
## S4 method for signature 'experiment' organism(object)
object |
an ORFik |
character, name of organism
Other ORFik_experiment:
ORFik.template.experiment.zf()
,
ORFik.template.experiment()
,
bamVarName()
,
create.experiment()
,
experiment-class
,
filepath()
,
libraryTypes()
,
outputLibs()
,
read.experiment()
,
save.experiment()
,
validateExperiments()
# 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))