lookup_biosamples: Retrieve sample annotations from NCBI's Biosample database
In denalitherapeutics/archs4: Wrappers to query and extract ARCHS4 data

Description Usage Arguments Value Source Examples

This function uses the rentrez package to retrieve sample annotations from NCBI's Biosample database.

1	lookup_biosamples(x, retmax = 1e+05 - 1L)

`x`	Character vector of sample identifiers to search the Biosample database for. Typically either `BioSample (SAMN)`, `SRA (SRS)` or `GEO (GSM)` accession numbers.
`retmax`	Scalar integer, the maximum number of (total) matches to retrieve from Entrez. See https://www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_ESearch_ for details. The number of records that can be retrieved in one query must be < 100,000.

A tbl_df data.frame with sample annotations. Column names and numbers vary depending on the attributes available in the Biosample database.

https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4_ESearch

if (interactive()) {
 # BioSample identifiers
 lookup_biosamples(c("GSM1947162", "GSM1947179"))
 # mixed SRS and GSM identifiers
 lookup_biosamples(c("SRS1171537", "SRS1171536", "GSM1947179"))
 # mixed samples from two different studies (with different attributes)
 lookup_biosamples(c("SRS1171537", "SRS1271536"))
}