read.experiment {ORFik} | R Documentation

## Read ORFik `experiment`

### 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/",
      validate = TRUE
    )

### 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.
`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!

### Value

an ORFik `experiment`

### See Also

Other ORFik_experiment: `ORFik.template.experiment.zf()`, `ORFik.template.experiment()`, `bamVarName()`, `create.experiment()`, `experiment-class`, `filepath()`, `libraryTypes()`, `organism,experiment-method`, `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/")

[Package ORFik version 1.14.7 Index]