create.experiment {ORFik} | R Documentation |
experiment
Create information on runs / samples from an experiment as a single R object. By using files in a folder. It will try to make an experiment table with information per sample. There will be several columns you can fill in, most of there it will try to auto-detect. Like if it is RNA-seq or Ribo-seq, Wild type or mutant etc. You will have to fill in the details that were not autodetected. Easiest way to fill in the blanks are in a csv editor like libre Office or excel. Remember that each row (sample) must have a unique combination of values. An extra column called "reverse" is made if there are paired data, like +/- strand wig files.
create.experiment( dir, exper, saveDir = NULL, types = c("bam", "bed", "wig"), txdb = "", fa = "", viewTemplate = TRUE )
dir |
Which directory to create experiment from |
exper |
Short name of experiment, max 5 characters long |
saveDir |
Directory to save experiment csv file (NULL) |
types |
Default (bam, bed, wig), which types of libraries to allow |
txdb |
A path to gff/gtf file used for libraries |
fa |
A path to fasta genome/sequences used for libraries |
viewTemplate |
run View() on template when finished, default (TRUE) |
a data.frame, NOTE: this is not a ORFik experiment, only a template for it!
Other ORFik_experiment:
bamVarName()
,
experiment-class
,
libraryTypes()
,
outputLibs()
,
read.experiment()
,
save.experiment()
,
validateExperiments()
# 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 df <- read.experiment(template) # Save with: save.experiment(df, file = "path/to/save/experiment.csv")