Search the SRA database and create a data frame of sample metadata

Usage

create_sample_info(term, retmax = 5000)

Arguments

term: Character with the search term, e.g. "Glycine max[ORGN] AND RNA-seq[STRA]".
retmax: Numeric with the maximum number of hits returned by the search.

Value

A data frame with the following columns:

BioSample: BioSample accession.
Experiment: Experiment accession (SRX*).
Run: Run accession (SRR*).
Tissue: Tissue from which RNA was extracted.
Pubmed: Pubmed ID of articles associated with the project, if any.
BioProject: Bioproject accession.
Instrument: Sequencing instrument
Layout: Library layout (single- or paired-end sequencing).
Selection_method: Library selection method.
SRA_sample: SRA sample accession (SRS*).
SRA_study: SRA study accession (SRP*).
Treatment: Treatment for the biosample.
Cultivar: Plant cultivar.
Study_title: Study title, if any.
Study_abstract: Study abstract, if any.
Date: Date of release.
Origin: Country of origin.

Examples

term <- "SAMN02422669[BSPL]"
df <- create_sample_info(term)
#> Error in curl::curl_fetch_memory(url, handle = handle): Timeout was reached: [eutils.ncbi.nlm.nih.gov] Connection timed out after 10001 milliseconds