read.experiment: Read ORFik 'experiment'

In ORFik: Open Reading Frames in Genomics

Description

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

Usage

read.experiment(file, in.dir = "~/Bio_data/ORFik_experiments/")

Arguments

file	relative path to a ORFik experiment. That is a .csv file following ORFik experiment style ("," as seperator). , or a template data.frame from create.experiment. Can also be full path to file, then in.dir argument is ignored.
in.dir	Directory to load experiment csv file from, default: "~/Bio_data/ORFik_experiments/" Set to NULL if you don't want to save it to disc. Does not apply if file is not a path, but a data.frame. Also does not apply if file was given as full path.

Value

an ORFik experiment

See Also

Other ORFik_experiment: ORFik.template.experiment(), bamVarName(), create.experiment(), experiment-class, filepath(), libraryTypes(), organism.df(), outputLibs(), save.experiment(), validateExperiments()

Examples

# 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/")

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