create.experiment {ORFik}R Documentation

Create a template for new ORFik experiment

Description

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.

Usage

create.experiment(
  dir,
  exper,
  saveDir = NULL,
  types = c("bam", "bed", "wig"),
  txdb = "",
  fa = "",
  viewTemplate = TRUE
)

Arguments

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)

Value

a data.frame, NOTE: this is not a ORFik experiment, only a template for it!

See Also

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

Examples

# 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")

[Package ORFik version 1.6.9 Index]