create.experiment: Create a ORFik 'experiment'
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value See Also Examples

Create information on runs / samples from an experiment as a single R object. By using files in a folder / folders. 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 auto detected. 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 = "~/Bio_data/ORFik_experiments/",
  txdb = "",
  fa = "",
  organism = "",
  pairedEndBam = FALSE,
  viewTemplate = TRUE,
  types = c("bam", "bed", "wig"),
  libtype = "auto",
  stage = "auto",
  rep = "auto",
  condition = "auto",
  fraction = "auto"
)

`dir`	Which directory / directories to create experiment from
`exper`	Short name of experiment, max 5 characters long
`saveDir`	Directory to save experiment csv file, default: "~/Bio_data/ORFik_experiments/" Set to NULL if you don't want to save it to disc.
`txdb`	A path to gff/gtf file used for libraries
`fa`	A path to fasta genome/sequences used for libraries, remember the file must have a fasta index too.
`organism`	character, default: "" (no organism set), scientific name of organism. Homo sapiens, Danio rerio, Rattus norvegicus etc. If you have a SRA metadata csv file, you can set this argument to study$ScientificName[1], where study is the SRA metadata for all files that was aligned.
`pairedEndBam`	logical FALSE, else TRUE, or a logical list of TRUE/FALSE per library you see will be included (run first without and check what order the files will come in) 1 paired end file, then two single will be c(T, F, F). If you have a SRA metadata csv file, you can set this argument to study$LibraryLayout == "PAIRED", where study is the SRA metadata for all files that was aligned.
`viewTemplate`	run View() on template when finished, default (TRUE)
`types`	Default (bam, bed, wig), which types of libraries to allow
`libtype`	character, default "auto". Library types, must be length 1 or equal length of number of libraries. "auto" means ORFik will try to guess from file name.
`stage`	character, default "auto". Developmental stage, tissue or cell line, must be length 1 or equal length of number of libraries. "auto" means ORFik will try to guess from file name.
`rep`	character, default "auto". Replicate numbering, must be length 1 or equal length of number of libraries. "auto" means ORFik will try to guess from file name.
`condition`	character, default "auto". Library conditions, must be length 1 or equal length of number of libraries. "auto" means ORFik will try to guess from file name.
`fraction`	character, default "auto". Fractionation of library, must be length 1 or equal length of number of libraries. "auto" means ORFik will try to guess from file name.

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

Other ORFik_experiment: ORFik.template.experiment(), bamVarName(), experiment-class, filepath(), libraryTypes(), organism.df(), 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")
# 4. Pick fasta genome of organism
fa <- system.file("extdata", "genome.fasta", package = "ORFik")
# 5. Set organism (optional)
org <- "Homo sapiens"

# Create temple not saved on disc yet:
template <- create.experiment(dir = dir, exper, txdb = txdb,
                              saveDir = NULL,
                              fa = fa, organism = org,
                              viewTemplate = FALSE)
## Now fix non-unique rows: either is libre office, microsoft excel, or in R
template$X5[6] <- "heart"
# read experiment (if you set correctly)
df <- read.experiment(template)
# Save with: save.experiment(df, file = "path/to/save/experiment.csv")

## Create and save experiment directly:
## Default location: "~/Bio_data/ORFik_experiments/"
#template <- create.experiment(dir = dir, exper, txdb = txdb,
#                               fa = fa, organism = org,
#                               viewTemplate = FALSE)
## Custom location
#template <- create.experiment(dir = dir, exper, txdb = txdb,
#                               saveDir = "~/MY/CUSTOME/LOCATION",
#                               fa = fa, organism = org,
#                               viewTemplate = FALSE)