find_url_ebi_safe: Find URL for EBI fastq files

In Roleren/ORFik: Open Reading Frames in Genomics

Find URL for EBI fastq files

Description

Safer version

Usage

find_url_ebi_safe(
  accession,
  SRR = NULL,
  stop.on.error = FALSE,
  ebi_file_format = c("fastq_ftp", "sra_ftp")[1],
  convert_to_ascp = FALSE
)

Arguments

accession	character: (PRJ, SRP, ERP, DRP, SRX, SRR, ERR,..). For studies or samples, it returns all runs per study or sample.
SRR	character, which SRR numbers to subset by (can also be ERR or DRR numbers)
stop.on.error	logical FALSE, if TRUE will stop if all files are not found. If FALSE returns empty character vector if error is catched.
ebi_file_format	character, format of run download, default is fastq (ftp): c("fastq_ftp", "sra_ftp")[1]
convert_to_ascp	logical, default FALSE. If TRUE use server: [e-mail]:

Value

character (1 element per SRR number)

Roleren/ORFik documentation built on April 12, 2025, 5:31 a.m.