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)

### Arguments

`file` | a .csv file following ORFik experiment style ("," as seperator) , or a template data.frame from `create.experiment`

### Value

an ORFik `experiment`

### See Also

Other ORFik_experiment: `bamVarName()`, `create.experiment()`, `experiment-class`, `libraryTypes()`, `outputLibs()`, `save.experiment()`, `validateExperiments()`

### Examples

    # From file
    ## Not run:
    # Read from file
    df <- read.experiment(filepath) # <- valid .csv file

    ## End(Not run)
    # Read from (create.experiment() template)
    # 1. Pick directory
    dir <- system.file("extdata", "", package = "ORFik")
    # 2. Pick an experiment name
    exper <- "ORFik"
    # 3. Pick .gff/.gtf location
    txdb <- system.file("extdata", "annotations.gtf", package = "ORFik")
    template <- create.experiment(dir = dir, exper, txdb = txdb,
                                  viewTemplate = FALSE)
    template$X5[6] <- "heart" # <- fix non unique row
    # read experiment from template
    df <- read.experiment(template)

    # To save it, do:
    # save.experiment(df, file = "path/to/save/experiment.csv")

[Package ORFik version 1.6.9 Index]