View source: R/experiment_IO.R
read.experiment | R Documentation |
experiment
Read in runs / samples from an experiment as a single R object.
To read an ORFik experiment, you must of course make one first.
See create.experiment
The file must be csv and be a valid ORFik experiment
read.experiment(
file,
in.dir = ORFik::config()["exp"],
validate = TRUE,
output.env = .GlobalEnv
)
file |
relative path to a ORFik experiment. That is a .csv file following
ORFik experiment style ("," as seperator).
, or a template data.frame from |
in.dir |
Directory to load experiment csv file from, default:
|
validate |
logical, default TRUE. Abort if any library files does not exist. Do not set this to FALSE, unless you know what you are doing! |
output.env |
an environment, default .GlobalEnv. Which environment
should ORFik output libraries to (if this is done),
can be updated later with |
an ORFik experiment
Other ORFik_experiment:
ORFik.template.experiment()
,
ORFik.template.experiment.zf()
,
bamVarName()
,
create.experiment()
,
experiment-class
,
filepath()
,
libraryTypes()
,
organism,experiment-method
,
outputLibs()
,
save.experiment()
,
validateExperiments()
# From file
## Not run:
# Read from file
df <- read.experiment(filepath) # <- valid ORFik .csv file
## End(Not run)
## Read from (create.experiment() template)
df <- ORFik.template.experiment()
## To save it, do:
# save.experiment(df, file = "path/to/save/experiment")
## You can then do:
# read.experiment("path/to/save/experiment")
# or (identical):
# read.experiment("experiment", in.dir = "path/to/save/")
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