list.experiments {ORFik} | R Documentation

## List current experiment available

### Description

Will only search .csv extension, also exclude any experiment with the word template.

### Usage

    list.experiments(
      dir = "~/Bio_data/ORFik_experiments/",
      pattern = "*",
      libtypeExclusive = NULL,
      validate = TRUE,
      BPPARAM = bpparam()
    )

### Arguments

`dir` | directory for ORFik experiments: default: "~/Bio_data/ORFik_experiments/"
`pattern` | allowed patterns in experiment file name: default ("*", all experiments)
`libtypeExclusive` | search for experiments with exclusivly this libtype, default (NULL, all)
`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!
`BPPARAM` | how many cores/threads to use? default: bpparam()

### Value

a data.table, 1 row per experiment with columns:
- experiment (name),
- organism
- author
- libtypes
- number of samples

### Examples

    ## Make your experiments
    df <- ORFik.template.experiment(TRUE)
    df2 <- df[1:6,] # Only first 2 libs
    ## Save them
    # save.experiment(df, "~/Bio_data/ORFik_experiments/exp1.csv")
    # save.experiment(df2, "~/Bio_data/ORFik_experiments/exp1_subset.csv")
    ## List all experiment you have:
    ## Path above is default path, so no dir argument needed
    #list.experiments()
    #list.experiments(pattern = "subset")
    ## For non default directory experiments
    #list.experiments(dir = "MY/CUSTOM/PATH)

[Package ORFik version 1.14.7 Index]