| organism.df {ORFik} | R Documentation |
Uses the txdb / gtf organism information, if existing.
organism.df(df)
df |
an ORFik |
organism (character vector), if no organism set: NA
Other ORFik_experiment:
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(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))