Resolve a GEO accession to its SRA accessions

Maps a GEO Series (GSE) or Sample (GSM) to the underlying Sequence Read Archive (SRA) accessions — study (SRP), experiment (SRX), run (SRR), and sample (SRS) — by cross-referencing NCBI Entrez (gds -> sra). This is the accession-linking bridge to raw sequencing data; it downloads no sequence files.

Usage

geoToSRA(geo)

Arguments

geo: character(1), a GEO accession (GSE... or GSM...).

Value

A data.frame with one row per SRA run and columns geo_accession, srp, srx, srr, srs. Returns a zero-row data.frame (same columns) when the accession has no linked SRA records.

Details

Uses the NCBI Entrez API through rentrez. An ENTREZ_KEY raises the rate limit; see searchGEO for how to set one.

Examples

if (FALSE) { # \dontrun{
geoToSRA("GSE164073")
} # }