read.experiment {ORFik} | R Documentation |
experiment
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
read.experiment(file)
file |
a .csv file following ORFik experiment style ("," as seperator)
, or a template data.frame from |
an ORFik experiment
Other ORFik_experiment:
bamVarName()
,
create.experiment()
,
experiment-class
,
libraryTypes()
,
outputLibs()
,
save.experiment()
,
validateExperiments()
# 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")