config.exper: Set directories for experiment

In JokingHero/ORFik: Open Reading Frames in Genomics

Set directories for experiment

Description

Defines a folder for: 1. fastq files (raw_data)
2. bam files (processed data)
3. references (organism annotation and STAR index)
4. Experiment (name of experiment)

Usage

config.exper(
  experiment,
  assembly,
  type,
  config = ORFik::config(),
  sub_dir_single = file.path(type, experiment, ""),
  name_with_type_suffix = TRUE
)

Arguments

experiment	short name of experiment (must be valid as a folder name)
assembly	name of organism and assembly (must be valid as a folder name)
type	name of sequencing type, Ribo-seq, RNA-seq, CAGE.. Can be more than one.
config	a named character vector of length 3, default: ORFik::config()
sub_dir_single	character, path. Default: file.path(type, experiment, "") The subdirectory relative to config defined main locations. If defined location should be used directly without making subdirectories, set to "".
name_with_type_suffix	logical, default TRUE. Make fastq name like 'fastq RNA-seq', setting it to FALSE gives name 'fastq'. Only allowed when length(type) == 1

Value

named character vector of paths for experiment

Examples

# Where should files go in general?
ORFik::config()
# Paths for project: "Alexaki_Human" containing Ribo-seq and RNA-seq:
#config.exper("Alexaki_Human", "Homo_sapiens_GRCh38_101", c("Ribo-seq", "RNA-seq"))

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.