Check if FASTQ files were properly downloaded
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)
#> Run Status
#> 1 SRR1039508 OK
fastq_exists(sample_info, fastqdir, collapse_pe = FALSE)
#> Run Status
#> 1 SRR1039508_1 OK
#> 2 SRR1039508_2 OK