fastq_exists: Check if FASTQ files were properly downloaded

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

Check if FASTQ files were properly downloaded

Description

Check if FASTQ files were properly downloaded

Usage

fastq_exists(
  sample_info = NULL,
  fastqdir = "results/01_FASTQ_files",
  collapse_pe = TRUE
)

Arguments

sample_info	Data frame of sample metadata created with the function create_sample_info.
fastqdir	Path to the directory where .fastq files will be stored. Default: results/01_FASTQ_files.
collapse_pe	Logical scalar indicating whether to collapse paired-end files runs into a single run. If TRUE (default), files like SRR12345_1.fastq.gz and SRR12345_2.fastq.gz will be collapsed to SRR12345.

Value

Data frame with run accession in the first column, and status in the second column. If the FASTQ file for a given run exists, its status will be "OK", otherwise it will be NA.

Examples

data(sample_info)
fastqdir <- system.file("extdata", package = "bears")
fastq_exists(sample_info, fastqdir)
fastq_exists(sample_info, fastqdir, collapse_pe = FALSE)

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.