create.experiment: Create a ORFik 'experiment'

Description Usage Arguments Value See Also Examples

View source: R/experiment.R

Description

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.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
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"
)

Arguments

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.

Value

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

See Also

Other ORFik_experiment: ORFik.template.experiment(), bamVarName(), experiment-class, filepath(), libraryTypes(), organism.df(), outputLibs(), read.experiment(), save.experiment(), validateExperiments()

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
# 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)

ORFik documentation built on March 27, 2021, 6 p.m.