list.experiments: List current experiment available

In Roleren/ORFik: Open Reading Frames in Genomics

List current experiment available

Description

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

Usage

list.experiments(
  dir = ORFik::config()["exp"],
  pattern = "*",
  libtypeExclusive = NULL,
  validate = TRUE,
  BPPARAM = bpparam()
)

Arguments

dir	directory for ORFik experiments: default: ORFik::config()["exp"], which by default is: "~/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)

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.