create_dir_structure: Create a standard directory for bears

In almeidasilvaf/bear: Building Expression Atlas from RNA-Seq data

Create a standard directory for bears

Description

Create a standard directory for bears

Usage

create_dir_structure(rootdir = NULL)

Arguments

rootdir

Root directory where all subdirectories will be created. If not specified, a directory named "results_YYYY-MM-DD" will be created, where Y, M and D represent year, month and day, respectively.

Value

A list of paths with following elements:

fastqdir

Path to directory where FASTQ files are.

qcdir

Path to directory where QC and summary statistics will be stored.

filtdir

Path to directory where filtered FASTQ files are.

mappingdir

Path to directory where STAR-derived BAM files are.

salmonindex

Path to directory where salmon transcriptome index is.

salmondir

Path to directory where salmon output files are.

kallistoindex

Path to directory where kallisto transcriptome index is.

kallistodir

Path to directory where kallisto output files are.

fcountsdir

Path to directory where featureCounts output files are.

stringtiedir

Path to directory where StringTie output files are.

Examples

rootdir <- tempdir()
dirs <- create_dir_structure(rootdir)

almeidasilvaf/bear documentation built on April 14, 2023, 7:03 p.m.