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())

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()

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 April 23, 2024, 12:37 a.m.