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 / 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/" |
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)