config: Read directory config for ORFik experiments

In Roleren/ORFik: Open Reading Frames in Genomics

Read directory config for ORFik experiments

Description

Defines a folder for: 1. fastq files (raw data)
2. bam files (processed data)
3. references (organism annotation and STAR index)
4. experiments (Location to store and load all experiment .csv files) Update or use another config using config.save() function.

Usage

config(
  file = config_file(old_config_location = old_config_location),
  old_config_location = "~/Bio_data/ORFik_config.csv"
)

Arguments

file	location of config csv, default: config_file(old_config_location = old_config_location)
old_config_location	path, old config location before BiocFileCache implementation. Will copy this to cache directory and delete old version. This is done to follow bioc rules on not writing to user home directory.

Value

a named character vector of length 3

Examples

## Make with default config path
#config()

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.