get_filereport: This function downloads the filereport of a study and saves...

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

Description

This function downloads the filereport of a study and saves it as an rda file in extdata. The intermediate file is deleted.

Usage

get_filereport(url, acc)

Arguments

url	Url of the filereport. The url of a filereport of a study can be gotten from the corresponding ebi metagenomic website by saving the link address of the 'TEXT' button (e.g. see https://www.ebi.ac.uk/ena/data/view/PRJEB8968)
acc	The study accession. This accession is also mentioned in the url (e.g. "PRJEB26733")

Value

The filereport as data frame. This is also stored as rda and can be loaded using load("extdata/filename")

Examples

get_filereport(url = "https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=PRJEB8968&result=read_run&fields=study_accession,sample_accession,secondary_sample_accession,experiment_accession,run_accession,tax_id,scientific_name,instrument_model,library_layout,fastq_ftp,fastq_galaxy,submitted_ftp,submitted_galaxy,sra_ftp,sra_galaxy,cram_index_ftp,cram_index_galaxy&download=txt",
acc = "PRJEB8968")

uashogeschoolutrecht/structural_colours documentation built on June 20, 2020, 4:07 p.m.